Professor Philip Hugenholtz
Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
Featured projects | Duration |
---|---|
High-throughput sequencing of protein variant libraries Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2023 |
Publications
Book Chapters
Davín, Adrián A., Schrempf, Dominik, Williams, Tom A., Hugenholtz, Philip and Szöllősi, Gergely J. (2022). Relative time inference using lateral gene transfers. Environmental microbial evolution: methods and protocols. (pp. 75-94) edited by Haiwei Luo. New York, United States: Humana Press. doi: 10.1007/978-1-0716-2691-7_4
Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029
Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastomonas: ProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00918
Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastobacter: ProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-11) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00800
Patel, Bharat K. C. and Hugenholtz, Philip (2015). Anaerobaculum. Bergey's Manual of Systematics of Archaea and Bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm01254
Tringe, Susannah G. and Hugenholtz, Philip (2011). The enduring legacy of small subunit rRNA in microbiology. Handbook of molecular microbial ecology I: metagenomics and complementary approaches. (pp. 123-128) Hoboken, New Jersey, USA: John Wiley & Sons. doi: 10.1002/9781118010518.ch15
Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplifications of uncultivated organisms. Uncultivated microorganisms. (pp. 83-100) edited by Slava S. Epstein. Heidelberg, Germany: Springer. doi: 10.1007/7171_2008_10
Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplification of uncultivated organisms. Uncultivated microorganisms. (pp. 241-256) edited by Slava S. Epstein. Heidelberg, Germany: Springer . doi: 10.1007/978-3-540-85465-4_10
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. Bergey's manual of systematic bacteriology. (pp. 452-459) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer.
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117. Bergey's manual of systematic bacteriology: The proteobacteria. Part C. The alpha-, beta-, delta-, and epsilonproteobacteria. (pp. 258-263) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer. doi: 10.1007/0-387-29298-5_70
Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. Encyclopedia of genetics, genomics, proteomics, and bioinformatics. (pp. 1386-1391) edited by Lynn B. Jorde. West Sussex, U.K.: John Wiley & Sons. doi: 10.1002/047001153X.g205313
Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, Philip, Pawlowski, J. and Simpson, A.G. (2004). The tree of life: An overview. Assembling the tree of life. (pp. 43-75) New York: Oxford University Press.
Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). Gene Probes - Principles and Protocols. (pp. 1-17) edited by Aquino de Muro. M and Rapley. R. London: Humana Press.
Journal Articles
Venter, Stephanus N., Rodriguez-R, Luis M., Chuvochina, Maria, Palmer, Marike, Hugenholtz, Philip and Steenkamp, Emma T. (2024). Options and considerations for validation of prokaryotic names under the SeqCode. Systematic and Applied Microbiology, 47 (6) 126554, 126554. doi: 10.1016/j.syapm.2024.126554
Williams, Tom A, Davin, Adrian A, Szánthó, Lénárd L, Stamatakis, Alexandros, Wahl, Noah A, Woodcroft, Ben J, Soo, Rochelle M, Eme, Laura, Sheridan, Paul O, Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip and Szöllősi, Gergely J (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18 (1) wrae129. doi: 10.1093/ismejo/wrae129
Mussig, Aaron J., Chaumeil, Pierre-Alain, Chuvochina, Maria, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2024). Putative genome contamination has minimal impact on the GTDB taxonomy. Microbial Genomics, 10 (5) 001256. doi: 10.1099/mgen.0.001256
Yu Jiao, Jian-, Abdugheni, Rashidin, Zhang, Dao-Feng, Ahmed, Iftikhar, Ali, Mukhtiar, Chuvochina, Maria, Dedysh, Svetlana N, Dong, Xiuzhu, Göker, Markus, Hedlund, Brian P, Hugenholtz, Philip, Jangid, Kamlesh, Liu, Shuang-Jiang, Moore, Edward R B, Rao, Manik Prabhu Narsing, Oren, Aharon, Rossello-Mora, Ramon, Rekadwad, Bhagwan Narayan, Salam, Nimaichand, Shu, Wensheng, Sutcliffe, Iain C, Teo, Wee Fei Aaron, Trujillo, Martha E, Venter, Stephanus N, Whitman, William B, Zhao, Guoping and Li, Wen-Jun (2024). Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data era. National Science Review, 11 (7) nwae168, nwae168. doi: 10.1093/nsr/nwae168
Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere, 9 (4), e0055523. doi: 10.1128/msphere.00555-23
Miliotis, Georgios, Sengupta, Pratyay, Hameed, Asif, Chuvochina, Maria, McDonagh, Francesca, Simpson, Anna C., Parker, Ceth W., Singh, Nitin K., Rekha, Punchappady D., Morris, Dearbháile, Raman, Karthik, Kyrpides, Nikos C., Hugenholtz, Philip and Venkateswaran, Kasthuri (2024). Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of
Tigheibacillus jepli
gen. nov., sp. nov. mBio, 15 (4), e0018124. doi: 10.1128/mbio.00181-24
Budden, Kurtis F, Shukla, Shakti D, Bowerman, Kate L, Vaughan, Annalicia, Gellatly, Shaan L, Wood, David L A, Lachner, Nancy, Idrees, Sobia, Rehman, Saima Firdous, Faiz, Alen, Patel, Vyoma K, Donovan, Chantal, Alemao, Charlotte A, Shen, Sj, Amorim, Nadia, Majumder, Rajib, Vanka, Kanth S, Mason, Jazz, Haw, Tatt Jhong, Tillet, Bree, Fricker, Michael, Keely, Simon, Hansbro, Nicole, Belz, Gabrielle T, Horvat, Jay, Ashhurst, Thomas, van Vreden, Caryn, McGuire, Helen, Fazekas de St Groth, Barbara ... Hansbro, Philip M (2024). Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut, 73 (5), gutjnl-2023. doi: 10.1136/gutjnl-2023-330521
Jones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2), e0337023. doi: 10.1128/mbio.03370-23
Field, Christian J., Bowerman, Kate L. and Hugenholtz, Philip (2024). Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microbial Genomics, 10 (1) 001176. doi: 10.1099/mgen.0.001176
Leong, Lex E X, Denman, Stuart E, Kang, Seungha, Mondot, Stanislas, Hugenholtz, Philip and McSweeney, Chris S (2023). - Invited Review - Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota. Animal bioscience, 37 (2), 396-403. doi: 10.5713/ab.23.0351
de la Haba, Rafael R., Arahal, David R., Sánchez-Porro, Cristina, Chuvochina, Maria, Wittouck, Stijn, Hugenholtz, Philip and Ventosa, Antonio (2023). A long-awaited taxogenomic investigation of the family Halomonadaceae. Frontiers in Microbiology, 14 1293707, 1-28. doi: 10.3389/fmicb.2023.1293707
Zhou, Joyce, Boyd, Joel A., Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L. A., Hugenholtz, Philip, Tyson, Gene W., Krause, Lutz and Ó Cuív, Páraic (2023). Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans. BMC Research Notes, 16 (1) 174, 1-4. doi: 10.1186/s13104-023-06447-3
Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Zaugg, Julian, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'. Microbial Genomics, 9 (8) 001092. doi: 10.1099/mgen.0.001092
McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology, 42 (5), 715-718. doi: 10.1038/s41587-023-01845-1
Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Skarshewski, Adam, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2023). Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiology Letters, 370 fnad071, 1-33. doi: 10.1093/femsle/fnad071
Williams, Tom A., Davín, Adrián A., Morel, Benoit, Szánthó, Lénárd L., Spang, Anja, Stamatakis, Alexandros, Hugenholtz, Philip and Szöllősi, Gergely J. (2023). Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biology and Evolution, 15 (7) evad134. doi: 10.1093/gbe/evad134
Krco, Stefan, Davis, Samuel J., Joshi, Pallav, Wilson, Liam A., Monteiro Pedroso, Marcelo, Douw, Andrew, Schofield, Christopher J., Hugenholtz, Philip, Schenk, Gerhard and Morris, Marc T. (2023). Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance. Frontiers in Chemistry, 11 1196073, 1196073. doi: 10.3389/fchem.2023.1196073
Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia. Microbial Genomics, 9 (6) 001039, 1-15. doi: 10.1099/mgen.0.001039
Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2
Blyton, Michaela D. J., Pascoe, Jack, Hynes, Emily, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Frontiers in Microbiology, 14 1085090, 1-13. doi: 10.3389/fmicb.2023.1085090
Bromfield, Jacoba Isobella, Hugenholtz, Philip, Frazer, Ian Hector, Khosrotehrani, Kiarash and Chandra, Janin (2023). Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?. Frontiers in Oncology, 13 1091379, 1091379. doi: 10.3389/fonc.2023.1091379
Yin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T. Y., Leung, Gabriel M., Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M., Walsh, Fiona, Berendonk, Thomas U., Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D., Bezuidenhout, Carlos, Picão, Renata C., Ahammad, Shaikh Z., Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J., Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy ... Zhang, Tong (2023). Toward a universal unit for quantification of antibiotic resistance genes in environmental samples. Environmental Science and Technology, 57 (26), 9713-9721. doi: 10.1021/acs.est.3c00159
McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1). Nature Biotechnology, 42 (5), 813-813. doi: 10.1038/s41587-023-02026-w
Budden, Kurtis F., Gellatly, Shaan L., Vaughan, Annalicia, Amorim, Nadia, Horvat, Jay C., Hansbro, Nicole G., Wood, David L. A., Hugenholtz, Philip, Dennis, Paul G., Wark, Peter A. B. and Hansbro, Philip M. (2022). Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in mice. International Journal of Molecular Sciences, 24 (1) 252, 1-12. doi: 10.3390/ijms24010252
Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38 (23), 5315-5316. doi: 10.1093/bioinformatics/btac672
Hedlund, Brian P., Chuvochina, Maria, Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain C., Venter, Stephanus N. and Whitman, William B. (2022). SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology, 7 (10), 1702-1708. doi: 10.1038/s41564-022-01214-9
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Ray, Angelique E. , Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2022). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils. Environmental Microbiology, 24 (9), 4491-4491. doi: 10.1111/1462-2920.16191
Whitman, William B., Chuvochina, Maria, Hedlund, Brian P., Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain and Venter, Stephanus N. (2022). Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology, 45 (5) 126305, 1-8. doi: 10.1016/j.syapm.2022.126305
Ray, Angelique E., Zaugg, Julian, Benaud, Nicole, Chelliah, Devan S., Bay, Sean, Wong, Hon Lun, Leung, Pok Man, Ji, Mukan, Terauds, Aleks, Montgomery, Kate, Greening, Chris, Cowan, Don A., Kong, Weidong, Williams, Timothy J., Hugenholtz, Philip and Ferrari, Belinda C. (2022). Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal, 16 (11), 1-14. doi: 10.1038/s41396-022-01298-5
Hallstrøm, Søren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R. and Riemann, Lasse (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16 (11), 2525-2534. doi: 10.1038/s41396-022-01299-4
Liu, Yongqin, Ji, Mukan, Yu, Tao, Zaugg, Julian, Anesio, Alexandre M., Zhang, Zhihao, Hu, Songnian, Hugenholtz, Philip, Liu, Keshao, Liu, Pengfei, Chen, Yuying, Luo, Yingfeng and Yao, Tandong (2022). A genome and gene catalog of glacier microbiomes. Nature Biotechnology, 40 (9), 1341-1348. doi: 10.1038/s41587-022-01367-2
Krueger, Annika, Mohamed, Ahmed, Kolka, Cathryn M., Stoll, Thomas, Zaugg, Julian, Linedale, Richard, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Frazer, Ian H. and Hill, Michelle M. (2022). Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress. Cancers, 14 (9) 2143, 2143. doi: 10.3390/cancers14092143
Raina, Jean-Baptiste, Lambert, Bennett S., Parks, Donovan H., Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I., Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W. and Seymour, Justin R. (2022). Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature, 605 (7908), 132-138. doi: 10.1038/s41586-022-04614-3
Krueger, Annika, Zaugg, Julian, Lachner, Nancy, Bialasiewicz, Seweryn, Lin, Lynlee L., Gabizon, Sharon, Sobarun, Priyamvada, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip and Frazer, Ian H. (2022). Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients. ISME Communications, 2 (1) 13, 13. doi: 10.1038/s43705-022-00095-7
Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6
Blyton, Michaela D. J., Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology, 24 (9), 4209-4219. doi: 10.1111/1462-2920.15884
Parks, Donovan H., Chuvochina, Maria, Rinke, Christian, Mussig, Aaron J., Chaumeil, Pierre-Alain and Hugenholtz, Philip (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50 (D1), D785-D794. doi: 10.1093/nar/gkab776
Blyton, Michaela D.J, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology, 24 (1), 475-493. doi: 10.1111/1462-2920.15858
Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5
Bramucci, Anna R., Focardi, Amaranta, Rinke, Christian, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Raina, Jean-Baptiste (2021). Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1 (1) 79. doi: 10.1038/s43705-021-00079-z
Wilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21
Bowerman, Kate L., Knowles, Sarah C. L., Bradley, Janette E., Baltrūnaitė, Laima, Lynch, Michael D. J., Jones, Kathryn M. and Hugenholtz, Philip (2021). Effects of laboratory domestication on the rodent gut microbiome. ISME Communications, 1 (1) 49, 49. doi: 10.1038/s43705-021-00053-9
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology, 23 (8), 4276-4294. doi: 10.1111/1462-2920.15610
Chiri, Eleonora, Nauer, Philipp A., Lappan, Rachael, Jirapanjawat, Thanavit, Waite, David W., Handley, Kim M., Hugenholtz, Philip, Cook, Perran L.M., Arndt, Stefan K. and Greening, Chris (2021). Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. Proceedings of the National Academy of Sciences of the United States of America, 118 (30) e2102625118, 1-8. doi: 10.1073/pnas.2102625118
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0
Rinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8
Nayfach, Stephen, Páez-Espino, David, Call, Lee, Low, Soo Jen, Sberro, Hila, Ivanova, Natalia N., Proal, Amy D., Fischbach, Michael A., Bhatt, Ami S., Hugenholtz, Philip and Kyrpides, Nikos C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology, 6 (7), 960-970. doi: 10.1038/s41564-021-00928-6
Bay, Sean K., Waite, David W., Dong, Xiyang, Gillor, Osnat, Chown, Steven L., Hugenholtz, Philip and Greening, Chris (2021). Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME Journal, 15 (11), 3339-3356. doi: 10.1038/s41396-021-01001-0
Coleman, Gareth A., Davín, Adrián A., Mahendrarajah, Tara A., Szánthó, Lénárd L., Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J. and Williams, Tom A. (2021). A rooted phylogeny resolves early bacterial evolution. Science, 372 (6542) eabe0511, eabe0511-+. doi: 10.1126/science.abe0511
Pribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2
Henden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375
Chen, Ya-Jou, Leung, Pok Man, Wood, Jennifer L., Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Franks, Ashley E., Cook, Perran L. M. and Greening, Chris (2021). Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal, 15 (10), 2986-3004. doi: 10.1038/s41396-021-00988-w
Parks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682
Hugenholtz, Philip, Chuvochina, Maria, Oren, Aharon, Parks, Donovan H. and Soo, Rochelle M. (2021). Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME Journal, 15 (7), 1879-1892. doi: 10.1038/s41396-021-00941-x
Ji, Mukan, Williams, Timothy J., Montgomery, Kate, Wong, Hon Lun, Zaugg, Julian, Berengut, Jonathan F., Bissett, Andrew, Chuvochina, Maria, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. The ISME Journal, 15 (9), 2692-2707. doi: 10.1038/s41396-021-00944-8
Moentadj, Rabia, Wang, Yiwen, Bowerman, Kate, Rehaume, Linda, Nel, Hendrik, O Cuiv, Paraic, Stephens, Juliette, Baharom, Amalina, Maradana, Muralidhara, Lakis, Vanessa, Morrison, Mark, Wells, Timothy, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2021). Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice. Annals of the Rheumatic Diseases, 80 (5) annrheumdis-2020-219009, annrheumdis-2020. doi: 10.1136/annrheumdis-2020-219009
Donner, Erica, Zamyadi, Arash, Jex, Aaron, Short, Michael, Drigo, Barbara, McCarthy, David, Crosbie, Nicholas, Ahmed, Warish, Mueller, Jochen, Thomas, Kevin, Monis, Paul, Keegan, Alex, Ginige, Maneesha, Hugenholtz, Philip, Tyson, Gene, Hill, Kelly and Blackall, Linda (2021). Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42 (1), 18-22. doi: 10.1071/ma21006
Campbell, B. C., Al Kouba, J., Timbrell, V., Noor, M. J., Massel, K., Gilding, E. K., Angel, N., Kemish, B., Hugenholtz, P., Godwin, I. D. and Davies, J. M. (2020). Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiome. Science of the Total Environment, 747 141189, 141189. doi: 10.1016/j.scitotenv.2020.141189
Schriml, Lynn M., Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A., Finn, Robert D., Hugenholtz, Philip, Hunter, Christopher I., Hurwitz, Bonnie L., Kyrpides, Nikos C., Meyer, Folker, Mizrachi, Ilene Karsch, Sansone, Susanna-Assunta, Sutton, Granger, Tighe, Scott and Walls, Ramona (2020). COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific Data, 7 (1) 188, 188. doi: 10.1038/s41597-020-0524-5
Bandara, H. M.H.N., Wood, D. L.A., Vanwonterghem, I., Hugenholtz, P., Cheung, B. P.K. and Samaranayake, L. P. (2020). Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing. Scientific Reports, 10 (1) 7769, 7769. doi: 10.1038/s41598-020-64761-3
Bowerman, Kate L., Rehman, Saima Firdous, Vaughan, Annalicia, Lachner, Nancy, Budden, Kurtis F., Kim, Richard Y., Wood, David L. A., Gellatly, Shaan L., Shukla, Shakti D., Wood, Lisa G., Yang, Ian A., Wark, Peter A., Hugenholtz, Philip and Hansbro, Philip M. (2020). Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nature Communications, 11 (1) 5886, 1-15. doi: 10.1038/s41467-020-19701-0
Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 6 (1), 136-136. doi: 10.1038/s41564-020-00827-2
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea (Nature Biotechnology, (2020), 38, 9, (1079-1086), 10.1038/s41587-020-0501-8). Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0539-7
Ahmed, Warish, Angel, Nicola, Edson, Janette, Bibby, Kyle, Bivins, Aaron, O'Brien, Jake W., Choi, Phil M., Kitajima, Masaaki, Simpson, Stuart L., Li, Jiaying, Tscharke, Ben, Verhagen, Rory, Smith, Wendy J.M., Zaugg, Julian, Dierens, Leanne, Hugenholtz, Philip, Thomas, Kevin V. and Mueller, Jochen F. (2020). First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Science of the Total Environment, 728 138764, 138764. doi: 10.1016/j.scitotenv.2020.138764
Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina, Parks, Donovan H., Hugenholtz, Philip, Segata, Nicola, Kyrpides, Nikos C. and Finn, Robert D. (2020). A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology, 39 (1), 105-114. doi: 10.1038/s41587-020-0603-3
Ahmed, Warish, Bertsch, Paul M., Angel, Nicola, Bibby, Kyle, Bivins, Aaron, Dierens, Leanne, Edson, Janette, Ehret, John, Gyawali, Pradip, Hamilton, Kerry, Hosegood, Ian, Hugenholtz, Philip, Jiang, Guangming, Kitajima, Masaaki, Sichani, Homa T., Shi, Jiahua, Shimko, Katja M., Simpson, Stuart L., Smith, Wendy J. M., Symonds, Erin M., Thomas, Kevin V., Verhagen, Rory, Zaugg, Julian and Mueller, Jochen F (2020). Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers. Journal of Travel Medicine, 27 (5) ARTN taaa116, 1-11. doi: 10.1093/jtm/taaa116
Pedroso, Marcelo Monteiro, Waite, David W., Melse, Okke, Wilson, Liam, Mitić, Nataša, McGeary, Ross P., Antes, Iris, Guddat, Luke W., Hugenholtz, Philip and Schenk, Gerhard (2020). Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse. Protein and Cell, 11 (8), 613-617. doi: 10.1007/s13238-020-00736-4
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). A complete domain-to-species taxonomy for bacteria and archaea. Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0501-8
Carere, Carlo R., Steen, Jason A., Hugenholtz, Philip and Stott, Matthew B. (2020). Draft genome sequence of Limisphaera ngatamarikiensis NGM72.4(T), a moderately alkaliphilic thermophile belonging to the class Verrucomicrobiae. Microbiology Resource Announcements, 9 (18) e00225-20. doi: 10.1128/MRA.00225-20
Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, 36 (6), 1925-1927. doi: 10.1093/bioinformatics/btz848
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2020). Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 14 (3), 878-878. doi: 10.1038/s41396-019-0556-z
Bowerman, Kate L., Varelias, Antiopi, Lachner, Nancy, Kuns, Rachel D., Hill, Geoffrey R. and Hugenholtz, Philip (2020). Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. Gut Microbes, 11 (4), 1-17. doi: 10.1080/19490976.2019.1705729
Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5 (8), 987-994. doi: 10.1038/s41564-020-0733-x
Waite, David W., Chuvochina, Maria, Pelikan, Claus, Parks, Donovan H., Yilmaz, Pelin, Wagner, Michael, Loy, Alexander, Naganuma, Takeshi, Nakai, Ryosuke, Whitman, William B., Hahn, Martin W., Kuever, Jan and Hugenholtz, Philip (2020). Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. International Journal of Systematic and Evolutionary Microbiology, 70 (11) 004213, 5972-6016. doi: 10.1099/ijsem.0.004213
Budden, Kurtis F., Shukla, Shakti D., Rehman, Saima Firdous, Bowerman, Kate L., Keely, Simon, Hugenholtz, Philip, Armstrong-James, Darius P. H., Adcock, Ian M., Chotirmall, Sanjay H., Chung, Kian Fan and Hansbro, Philip M. (2019). Functional effects of the microbiota in chronic respiratory disease. Lancet Respiratory Medicine, 7 (10), 907-920. doi: 10.1016/S2213-2600(18)30510-1
Whitman, William B., Klenk, Hans-Peter, Arahal, David R., Aznar, Rosa, Garrity, George, Pester, Michael and Hugenholtz, Philip (2019). Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains. Microbiology Australia, 40 (3), 125-129. doi: 10.1071/MA19034
Blyton, Michaela D. J., Soo, Rochelle M., Whisson, Desley, Marsh, Karen J., Pascoe, Jack, Le Pla, Mark, Foley, William, Hugenholtz, Philip and Moore, Ben D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Animal Microbiome, 1 (1) 6, 6. doi: 10.1186/s42523-019-0008-0
Džunková, Mária, Low, Soo Jen, Daly, Joshua N., Deng, Li, Rinke, Christian and Hugenholtz, Philip (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4 (12), 2192-2203. doi: 10.1038/s41564-019-0526-2
Low, Soo Jen, Džunková, Mária, Chaumeil, Pierre-Alain, Parks, Donovan H. and Hugenholtz, Philip (2019). Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales. Nature Microbiology, 4 (8), 1306-1315. doi: 10.1038/s41564-019-0448-z
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Consent insufficient for data release Response. Science, 364 (6439), 446-446. doi: 10.1126/science.aax7509
Kessler, Adam J., Chen, Ya-Jou, Waite, David W., Hutchinson, Tess, Koh, Sharlynn, Popa, M. Elena, Beardall, John, Hugenholtz, Philip, Cook, Perran L. M. and Greening, Chris (2019). Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nature Microbiology, 4 (6), 1014-1023. doi: 10.1038/s41564-019-0391-z
Rehaume, Linda M., Matigian, Nicholas, Mehdi, Ahmed M., Lachner, Nancy, Bowerman, Kate L., Daly, Joshua, Lê Cao, Kim-Anh, Hugenholtz, Philip and Thomas, Ranjeny (2019). IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota. Annals of the Rheumatic Diseases, 78 (4), 494-503. doi: 10.1136/annrheumdis-2018-214381
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Toward unrestricted use of public genomic data. Science, 363 (6425), 350-352. doi: 10.1126/science.aaw1280
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7
Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2019). The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42 (1), 15-21. doi: 10.1016/j.syapm.2018.07.003
Soo, Rochelle M., Hemp, James and Hugenholtz, Philip (2019). Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radical Biology and Medicine, 140, 200-205. doi: 10.1016/j.freeradbiomed.2019.03.029
Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R ... Eloe-Fadrosh, Emiley A (2018). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37 (1), 29-37. doi: 10.1038/nbt.4306
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018). A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 13 (3), 663-675. doi: 10.1038/s41396-018-0282-y
Wood, David L. A., Lachner, Nancy, Tan, Jean-Marie, Tang, Stephanie, Angel, Nicola, Laino, Antonia, Linedale, Richard, Lê Cao, Kim-Anh, Morrison, Mark, Frazer, Ian H., Soyer, H. Peter and Hugenholtz, Philip (2018). A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes. MBio, 9 (5) e01432-18. doi: 10.1128/mBio.01432-18
Parks, Donovan H., Chuvochina, Maria, Waite, David W., Rinke, Christian, Skarshewski, Adam, Chaumeil, Pierre-Alain and Hugenholtz, Philip (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36 (10), 996-1004. doi: 10.1038/nbt.4229
Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018). Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 (7), 660-660. doi: 10.1038/nbt0718-660a
Waite, David W., Dsouza, Melissa, Sekiguchi, Yuji, Hugenholtz, Philip and Taylor, Michael W. (2018). Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. Scientific Reports, 8 (1) 8128, 8128. doi: 10.1038/s41598-018-26484-4
Laloo, Andrew E., Wei, Justin, Wang, Dongbo, Narayanasamy, Shaman, Vanwonterghem, Inka, Waite, David, Steen, Jason, Kaysen, Anne, Heintz-Buschart, Anna, Wang, Qilin, Schulz, Benjamin, Nouwens, Amanda, Wilmes, Paul, Hugenholtz, Philip, Yuan, Zhiguo and Bond, Philip L. (2018). Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid. Environmental science & technology, 52 (9), 5386-5397. doi: 10.1021/acs.est.7b04273
McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua ... Knight, Rob (2018). American gut: an open platform for citizen science microbiome research. mSystems, 3 (3) e00031-18. doi: 10.1128/mSystems.00031-18
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772
Varelias, Antiopi, Bunting, Mark D., Ormerod, Kate L., Koyama, Motoko, Olver, Stuart D., Straube, Jasmin, Kuns, Rachel D., Robb, Renee J., Henden, Andrea S., Cooper, Leanne, Lachner, Nancy, Gartlan, Kate H., Lantz, Olivier, Kjer-Nielsen, Lars, Mak, Jeffrey Y. W., Fairlie, David P., Clouston, Andrew D., McCluskey, James, Rossjohn, Jamie, Lane, Steven W., Hugenholtz, Philip and Hill, Geoffrey R. (2018). Recipient mucosal-associated invariant T cells control GVHD within the colon. Journal of Clinical Investigation, 128 (5), 1919-1936. doi: 10.1172/JCI91646
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Goeker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2018). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Nature Biotechnology, 36 (4), 368-368. doi: 10.1038/nbt0418-368c
Schofield, Benjamin J., Lachner, Nancy, Le, Oanh T., McNeill, David M., Dart, Peter, Ouwerkerk, Diane, Hugenholtz, Philip and Klieve, Athol V. (2018). Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57. Journal of Applied Microbiology, 124 (3), 855-866. doi: 10.1111/jam.13688
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 (2), 253-253. doi: 10.1038/s41564-017-0083-5
Ji, Mukan, Greening, Chris, Vanwonterghem, Inka, Carere, Carlo R., Bay, Sean K., Steen, Jason A., Montgomery, Kate, Lines, Thomas, Beardall, John, van Dorst, Josie, Snape, Ian, Stott, Matthew B., Hugenholtz, Philip and Ferrari, Belinda C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552 (7685), 400-403. doi: 10.1038/nature25014
Yeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8
Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017). Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, 1-32. doi: 10.7717/peerj.4075
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 (11), 1533-1542. doi: 10.1038/s41564-017-0012-7
Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Stocker, Roman (2017). A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2 (10), 1344-1349. doi: 10.1038/s41564-017-0010-9
Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A. and Schenk, Gerhard (2017). Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9 (8), 1157-1168. doi: 10.1039/c7mt00195a
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 (8), 725-731. doi: 10.1038/nbt.3893
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.. Nature Biotechnology, 35 (7), 676-683. doi: 10.1038/nbt.3886
Bissett, Andrew, Fitzgerald, Anna, Court, Leon, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I. ... Young, Andrew (2017). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016). Gigascience, 6 (5) gix021, 1-1. doi: 10.1093/gigascience/gix021
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017). Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8 (APR) 682 doi: 10.3389/fmicb.2017.00682.
Soo, Rochelle M. , Hemp, James, Parks, Donovan H. , Fischer, Woodward W. and Hugenholtz, Philip (2017). On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 (6332), 1436-1440. doi: 10.1126/science.aal3794
Chotirmall, Sanjay H., Gellatly, Shaan L., Budden, Kurtis F., Mac Aogain, Micheál, Shukla, Shakti D., Wood, David L. A., Hugenholtz, Philip, Pethe, Kevin and Hansbro, Philip M. (2017). Microbiomes in respiratory health and disease: an Asia-Pacific perspective. Respirology, 22 (2), 240-250. doi: 10.1111/resp.12971
Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A ., Hugenholtz, Philip and Hill, Geoffrey R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Blood, 129 (15), 2172-2185. doi: 10.1182/blood-2016-08-732628
Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016). Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 (1) 39114, 39114. doi: 10.1038/srep39114
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016). Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 (1) 37389, 37389. doi: 10.1038/srep37389
Budden, Kurtis F. , Gellatly, Shaan L. , Wood, David L., Cooper, Matthew A. , Morrison, Mark, Hugenholtz, Philip and Hansbro, Philip M. (2016). Emerging pathogenic links between microbiota and the gut-lung axis.. Nature Reviews Microbiology, 15 (1), 55-63. doi: 10.1038/nrmicro.2016.142
Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 (16170) 16170, 16170. doi: 10.1038/nmicrobiol.2016.170
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016). Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 (9) e2486, 1-28. doi: 10.7717/peerj.2486
Schofield, Benjamin J., Skarshewski, Adam, Lachner, Nancy, Ouwerkerk, Diane, Klieve, Athol V., Dart, Peter and Hugenholtz, Philip (2016). Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 11 (1) 60, 60. doi: 10.1186/s40793-016-0189-z
Ikeda-Ohtsubo, Wakako, Strassert, Juergen F. H., Kohler, Tim, Mikaelyan, Aram, Gregor, Ivan, Mchardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate and Brune, Andreas (2016). 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environmental Microbiology, 18 (8), 2548-2564. doi: 10.1111/1462-2920.13234
Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2
Haroon, Mohamed F., Thompson, Luke R., Parks, Donovan H., Hugenholtz, Philip and Stingl, Ulrich (2016). A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data, 3 (1) 160050, 160050.1-160050.6. doi: 10.1038/sdata.2016.50
Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat ... Young, Andrew (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 (1) 21, 21.1-21.11. doi: 10.1186/s13742-016-0126-5
Hugenholtz, Philip, Skarshewski, Adam and Parks, Donovan H. (2016). Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspectives in Biology, 8 (6) a018085, a018085. doi: 10.1101/cshperspect.a018085
Simpson, Jodie L., Daly, Joshua, Baines, Katherine J., Yang, Ian A., Upham, John W., Reynolds, Paul N., Hodge, Sandra, James, Alan L., Hugenholtz, Philip, Willner, Dana and Gibson, Peter G. (2016). Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. European Respiratory Journal, 47 (3), 792-800. doi: 10.1183/13993003.00405-2015
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip and Muyzer, Gerard (2016). Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology, 7 (FEB) 211, 211.1-211.18. doi: 10.3389/fmicb.2016.00211
Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016). High-resolution phylogenetic microbial community profiling. ISME Journal, 10 (8), 2020-2032. doi: 10.1038/ismej.2015.249
Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016). A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 (JAN) 1469, 1469.1-1469.15. doi: 10.3389/fmicb.2015.01469
Yeoh, Yun Kit, Sekiguchi, Yuji, Parks, Donovan H. and Hugenholtz, Philip (2015). Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Molecular Biology and Evolution, 33 (4), 915-927. doi: 10.1093/molbev/msv281
Lu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015). Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 (11) e0142720, e0142720.1-e0142720.10. doi: 10.1371/journal.pone.0142720
Matsuura, Norihisa, Tourlousse, Dieter M., Ohashi, Akiko, Hugenholtz, Philip and Sekiguchia, Yuji (2015). Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi. Genome Announcements, 3 (5) e00975-15. doi: 10.1128/genomeA.00975-15
Ormerod, Kate L., George, Narelle M., Fraser, James A., Wainwright, Claire and Hugenholtz, Philip (2015). Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ, 3 (9) e1223, e1223.1-e1223.27. doi: 10.7717/peerj.1223
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 (7), 1043-1055. doi: 10.1101/gr.186072.114
Leong, Lex E. X., Denman, Stuart E., Hugenholtz, Philip and McSweeney, Christopher S. (2015). Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions. Microbial Ecology, 71 (2), 494-504. doi: 10.1007/s00248-015-0641-4
Yeoh, Yun Kit, Paungfoo-Lonhienne, Chanyarat, Dennis, Paul G., Robinson, Nicole, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2015). The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.. Environmental Microbiology, 18 (5), 1338-1351. doi: 10.1111/1462-2920.12925
Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguamg, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip and Kyrpides, Nikos C. (2015). Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences, 10 (26) 26, 26. doi: 10.1186/s40793-015-0017-x
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015). Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 (1), 50-60. doi: 10.1128/jmbe.v16i1.816
Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015). Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 (5) e968, Art. No.: e968-Art. No.: e968. doi: 10.7717/peerj.968
Paungfoo-Lonhienne, Chanyarat, Yeoh, Yun Kit, Kasinadhuni, Naga Rup Pinaki, Lonhienne, Thierry G. A., Robinson, Nicole, Hugenholtz, Philip, Ragan, Mark A. and Schmidt, Susanne (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.. Scientific Reports, 5 (8678) 8678, 1-6. doi: 10.1038/srep08678
Abdul Rahman, Nurdyana, Parks, Donovan H., Willner, Dana L., Engelbrektson, Anna L., Goffredi, Shana K., Warnecke, Falk, Scheffrahn, Rudolf H. and Hugenholtz, Philip (2015). A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome, 3 (5) 5, 1-16. doi: 10.1186/s40168-015-0067-8
Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015). First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 (e740) e740, 1-24. doi: 10.7717/peerj.740
Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren, Land, Miriam, Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John C., Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C. and Klenk, Hans-Peter (2014). Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Standards in Genomic Sciences, 9 (1) 10, 10. doi: 10.1186/1944-3277-9-10
Chambers, Daniel C., Gellatly, Shaan L., Hugenholtz, Philip and Hansbro, Philip M. (2014). JTD special edition 'Hot Topics in COPD'- the microbiome in COPD. Journal of Thoracic Disease, 6 (11), 1525-1531. doi: 10.3978/j.issn.2072-1439.2014.11.08
Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014). GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 (1) e603, 1-16. doi: 10.7717/peerj.603
Kyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Goker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chun, Jongsik, Colwell, Rita R., Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F., Detter, John C., De Vos, Paul, Donohue, Timothy J., Dong, Xiu-Zhu, Ehrlich, Dusko S., Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Jansson, Janet K., Keasling, Jay D., Knight, Rob, Labeda, David, Lapidus, Alla ... Klenk, Hans-Peter (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12 (8) e1001920, e1001920.1-e1001920.7. doi: 10.1371/journal.pbio.1001920
Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 (21), 3123-3124. doi: 10.1093/bioinformatics/btu494
Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online (10), 1-14. doi: 10.1038/ismej.2014.50
Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073
Angly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014). CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 (11) 11, 11. doi: 10.1186/2049-2618-2-11
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105
Willner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014). Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 (2) e01064-13, e01064-13.1-e01064-13.10. doi: 10.1128/mBio.01064-13
Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 (1) 3212, 3212.1-3212.7. doi: 10.1038/ncomms4212
Göker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja ... Lapidus, Alla (2014). Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. Standards in Genomic Sciences, 9 (3), 1105-1117. doi: 10.4056/sigs.3016383
Goeker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Feng, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2014). Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences, 9 (3), 1076-1088. doi: 10.4056/sigs.5138968
Clingenpeel, Scott, Schwientek, Patrick, Hugenholtz, Philip and Woyke, Tanja (2014). Effects of sample treatments on genome recovery via single-cell genomics. The ISME Journal, 8 (12), 2546-2549. doi: 10.1038/ismej.2014.92
Lonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014). Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 (2), 785-790. doi: 10.2135/cropsci2013.07.0488
Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip and Sullivan, Matthe B. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.. Nature, 513 (7517), 242-245 + 13. doi: 10.1038/nature13459
Vipin Madhavan, T. P., Steen, Jason A., Hugenholtz, Philip and Sakellaris, Harry (2014). Genome sequence of enterotoxigenic Escherichia coli strain B2C. Genome Announcements, 2 (2) e00247-14. doi: 10.1128/genomeA.00247-14
Braff, William A., Willner, Dana, Hugenholtz, Philip, Rabaey, Korneel and Buie, Cullen R. (2013). Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE, 8 (1) e76751, e76751.1-e76751.7. doi: 10.1371/journal.pone.0076751
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 (7468), 578-578. doi: 10.1038/nature12619
Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sur Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, Del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2013). Defining the core Arabidopsis thaliana root microbiome. Nature, 501 (7468 SUPPL.).
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 (7459), 431-437. doi: 10.1038/nature12352
D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013). Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 (7) e68465, e68465.1-e68465.11. doi: 10.1371/journal.pone.0068465
Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579
Willner, Dana and Hugenholtz, Philip (2013). From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays, 35 (5), 436-442. doi: 10.1002/bies.201200174
He, Shaomei, Ivanova, Natalia, Kirton, Edward, Allgaier, Martin, Bergin, Claudia, Scheffrahn, Rudolf H., Kyrpides, Nikos C., Warnecke, Falk, Tringe, Susannah G. and Hugenholtz, Philip (2013). Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One, 8 (4) e61126, e61126. doi: 10.1371/journal.pone.0061126
Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013). Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 (4) e1003031, e1003031.1-e1003031.18. doi: 10.1371/journal.pcbi.1003031
Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2013). Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012). Mbio, 4 (1). doi: 10.1128/mBio.00516-12
Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013). Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 (3), 628-634. doi: 10.4056/sigs.5068949
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Klenk, Hans-Peter (2013). Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences, 9 (1), 83-92. doi: 10.4056/sigs.4338002
Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Woyke, Tanja (2013). Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences, 9 (1), 57-70. doi: 10.4056/sigs.4237901
Garrity, George M., Banfield, Jill, Eisen, Jonathan, van der Lelie, Niels, McMahon, Trina, Rusch, Doug, Delong, Edward, Moran, Mary Ann, Currie, Cameron, Furhman, Jed, Hallam, Steve, Hugenholtz, Phil, Moran, Nancy, Nelson, Karen, Roberts, Richard and Stepanauskas, Ramunas (2013). Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences, 8 (3), 561-570. doi: 10.4056/sigs.4638348
Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Klenk, Hans-Peter (2013). Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva. Standards in Genomic Sciences, 8 (2), 228-238. doi: 10.4056/sigs.3617113
Liolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences, 8 (2), 165-176. doi: 10.4056/sigs.3607108
Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip ... Lapidus, Alla (2013). Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences, 8 (2), 177-187. doi: 10.4056/sigs.3637201
Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Standards in Genomic Sciences, 8 (1), 47-57. doi: 10.4056/sigs.3547050
Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2013). Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences, 8 (1), 26-36. doi: 10.4056/sigs.3527032
Abt, Birte, Goeker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan ... Klenk, Hans-Peter (2013). Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Trep. Standards in Genomic Sciences, 8 (1), 88-105. doi: 10.4056/sigs.3096473
Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2013). Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences, 8 (1), 15-25. doi: 10.4056/sigs.3507020
Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Bruce, David, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2013). High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Standards in Genomic Sciences, 8 (1), 37-46. doi: 10.4056/sigs.3537045
Flowers, Jason J., He, Shaomei, Malfatti, Stephanie, Glavina del Rio, Tijana, Tringe, Susannah G., Hugenholtz, Philip and McMahon, Katherine D. (2013). Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal, 7 (12), 2301-2314. doi: 10.1038/ismej.2013.117
Willner, Dana and Hugenholtz, Phil (2013). Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter, 35 (1), 1-9. doi: 10.1016/j.clinmicnews.2012.12.001
Willner, Dana L., Hugenholtz, Philip, Yerkovich, Stephanie T., Tan, Maxine E., Daly, Joshua N., Lachner, Nancy, Hopkins, Peter M. and Chambers, Daniel C. (2013). Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 187 (6), 640-647. doi: 10.1164/rccm.201209-1680OC
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 (7464), 567-570. doi: 10.1038/nature12375
Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013). In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531, 3-19. doi: 10.1016/B978-0-12-407863-5.00001-0
Harris, J. Kirk, Caporaso, J. Gregory, Walker, Jeffrey J., Spear, John R., Gold, Nicholas J., Robertson, Charles E., Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob and Pace, Norman R. (2013). Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME Journal, 7 (1), 50-60. doi: 10.1038/ismej.2012.79
Chappell, K.J., Brealey, J.C., Mackay, I.M., Bletchly, C., Hugenholtz, P., Sloots, T.P., Sly, P.D. and Young, P.R. (2013). Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children. Journal of Medical Microbiology & Diagnosis, S (1), 1-9. doi: 10.4172/2161-0703.S1-005
Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Ivanova, Natalia (2012). Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences, 7 (2), 210-220. doi: 10.4056/sigs.3117229
Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2012). Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging. Mbio, 3 (6) e00373-12. doi: 10.1128/mBio.00373-12
Hugenholtz, Phil (2012). Guest commentary: the human microbiome and the promise of clinical ecology. Microbiology Australia, 33 (3), 90-90.
Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sut Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488 (7409), 86-90. doi: 10.1038/nature11237
Anderson, Iain, Chertkov, Olga, Chen, Amy, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences, 6 (3), 293-303. doi: 10.4056/sigs.2736042
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012). Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 (12), e94.1-e94.8. doi: 10.1093/nar/gks251
Knight, Rob, Jansson, Janet, Field, Dawn, Fierer, Noah, Desai, Narayan, Fuhrman, Jed A., Hugenholtz, Phil, van der Lelie, Daniel, Meyer, Folker, Stevens, Rick, Bailey, Mark J., Gordon, Jeffrey I., Kowalchuk, George A. and Gilbert, Jack A. (2012). Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30 (6), 513-520. doi: 10.1038/nbt.2235
Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012). Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 (5), 245-246. doi: 10.1038/nmeth.1990
Willner, Dana, Daly, Joshua, Whiley, David, Grimwood, Keith, Wainwright, Claire E. and Hugenholtz, Philip (2012). Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One, 7 (4) e34605, e34605.1-e34605.12. doi: 10.1371/journal.pone.0034605
McDonald, Daniel, Price, Morgan N., Goodrich, Julia, Nawrocki, Eric P., DeSantis, Todd Z, Probst, Alexander, Andersen, Gary L, Knight, Rob and Hugenholtz, Philip (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME Journal, 6 (3), 610-618. doi: 10.1038/ismej.2011.139
Godoy-Vitorino, Filipa, Goldfarb, Katherine C., Karaoz, Ulas, Leal, Sara, Garcia-Amado, Maria A., Hugenholtz, Philip, Tringe, Susannah G., Brodie, Eoin L. and Dominguez-Bello, Maria Gloria (2012). Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME Journal, 6 (3), 531-541. doi: 10.1038/ismej.2011.131
Goeker, Markus, Saunders, Elisabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2012). Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences, 6 (2), 230-239. doi: 10.4056/sigs.2726028
Anderson, Iain, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2012). Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences, 6 (2), 174-184. doi: 10.4056/sigs.2746047
Anderson, Iain, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Chang, Yun-juan, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C. ... Klenk, Hans-Peter (2012). Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences, 6 (2), 155-164. doi: 10.4056/sigs.2665915
Abt, Birte, Han, Cliff, Scheuner, Carmen, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Goeker, Markus ... Detter, John C. (2012). Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov and emendations of the family Spirochaetaceae and the genus Sphaerochae. Standards in Genomic Sciences, 6 (2), 194-209. doi: 10.4056/sigs.2796069
Copeland, Alex, Zhang, Xiaojing, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Djao, Olivier D. Ngatchou, Goeker, Markus, Sikorski, Johannes, Tindall, Brian J. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences, 6 (2), 145-154. doi: 10.4056/sigs.2475579
Mavromatis, Konstantinos, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Bruce, David, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1). Standards in Genomic Sciences, 6 (2), 210-219. doi: 10.4056/sigs.2816096
Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2012). Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Standards in Genomic Sciences, 7 (1), 120-130. doi: 10.4056/sigs.3296896
Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Woyke, Tanja (2012). Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Standards in Genomic Sciences, 7 (1), 107-119. doi: 10.4056/sigs.3216895
Copeland, Alex, Gu, Wei, Yasawong, Montri, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Goker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2012). Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences, 6 (1), 21-30. doi: 10.4056/sigs.2435521
Copeland, Alex, Zeytun, Ahmet, Yassawong, Montri, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Mavromatis, Konstantinos, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus, Detter, John C. ... Lapidus, Alla (2012). Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT). Standards in Genomic Sciences, 6 (2), 240-250. doi: 10.4056/sigs.2756060
Huntemann, Marcel, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2012). Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences, 6 (2), 185-193. doi: 10.4056/sigs.2786069
Han, Cliff, Kotsyurbenko, Oleg, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes ... Detter, John C. (2012). Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences, 6 (1), 94-103. doi: 10.4056/sigs.2456004
Werner, Jeffrey J., Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z., Walters, William A., Caporaso, J. Gregory, Angenent, Largus T., Knight, Rob and Ley, Ruth E (2012). Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME Journal, 6 (1), 94-103. doi: 10.1038/ismej.2011.82
Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Woyke, Tanja (2011). Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). Standards in Genomic Sciences, 5 (3), 398-406. doi: 10.4056/sigs.2344929
Han, Cliff, Mwirichia, Romano, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus ... Detter, John C. (2011). Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T). Standards in Genomic Sciences, 4 (3), 371-380. doi: 10.4056/sigs.2004648
Reddy, Amitha P., Allgaier, Martin, Singer, Steven W., Hazen, Terry C., Simmons, Blake A., Hugenholtz, Philip and VanderGheynst, Jean S. (2011). Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and Bioengineering, 108 (9), 2088-2098. doi: 10.1002/bit.23176
Gladden, John M., Allgaier, Martin, Miller, Christopher S., Hazen, Terry C., VanderGheynst, Jean S., Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2011). Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Applied and Environmental Microbiology, 77 (16), 5804-5812. doi: 10.1128/AEM.00032-11
Pope, P. B., Smith, W., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C. and Morrison, M. (2011). Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science, 333 (6042), 646-648. doi: 10.1126/science.1205760
Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip and Tyson, Gene W. (2011). Phage encoded H-NS: A potential Achilles heel in the bacterial defence system. Plos One, 6 (5) e20095, e20095-1-e20095-7. doi: 10.1371/journal.pone.0020095
Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi., Chain, Patrick S. G., Charlson, Emily, Costello, Elizabeth K. ... Glockner, Frank Oliver (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29 (5), 415-420. doi: 10.1038/nbt.1823
Land, Miriam, Held, Brittany, Gronow, Sabine, Abt, Birte, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2011). Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139(T)). Standards in Genomic Sciences, 4 (2), 233-243. doi: 10.4056/sigs.1784330
Pati, Amrita, Abt, Birte, Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja ... Ivanova, Natalia (2011). Complete genome sequence of Cellulophaga lytica type strain (LIM-21(T)). Standards in Genomic Sciences, 4 (2), 221-232. doi: 10.4056/sigs.1774329
Pati, Amrita, Zhang, Xiaojing, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Röhl, Alina, Mwirichia, Romano, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Wirth, Reinhard, Göker, Markus, Woyke, Tanja ... Land, Miriam (2011). Complete genome sequence of Oceanithermus profundus type strain (506(T)). Standards in Genomic Sciences, 4 (2), 210-220. doi: 10.4056/sigs.1734292
Göker, Markus, Gronow, Sabine, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T)). Standards in Genomic Sciences, 4 (2), 200-209. doi: 10.4056/sigs.1714269
Gronow, Sabine, Held, Brittany, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja ... Eisen, Jonathan A. (2011). Complete genome sequence of Bacteroides salanitronis type strain (BL78(T)). Standards in Genomic Sciences, 4 (2), 191-199. doi: 10.4056/sigs.1704212
Wirth, Reinhard, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ioanna, Pagani, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Bilek, Yvonne, Hader, Thomas, Rohde, Manfred, Spring, Stefan ... Klenk, Hans-Peter (2011). Complete genome sequence of Desulfurococcus mucosus type strain (O7/1(T)). Standards in Genomic Sciences, 4 (2), 173-182. doi: 10.4056/sigs.1644004
Pukall, Rüdiger, Zeytun, Ahmet, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, J. Chris, Woyke, Tanja ... Klenk, Hans-Peter (2011). Complete genome sequence of Deinococcus maricopensis type strain (LB-34(T)). Standards in Genomic Sciences, 4 (2), 163-172. doi: 10.4056/sigs.1633949
Pagani, Ioanna, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Held, Brittany, Goodwin, Lynne, Liolios, Konstantinos, Ovchinikova, Galina, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Han, Cliff, Tapia, Roxanne, Ngatchou-Djao, Olivier D., Rohde, Manfred, Göker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Marivirga tractuosa type strain (H-43(T)). Standards in Genomic Sciences, 4 (2), 154-162. doi: 10.4056/sigs.1623941
Mavromatis, Konstantinos, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Gronow, Sabine, Woyke, Tanja ... Kyrpides, Nikos C. (2011). Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845(T)). Standards in Genomic Sciences, 4 (2), 144-153. doi: 10.4056/sigs.1553865
Zeytun, Ahmet, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Han, James, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Ngatchou-Djao, Olivier D., Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Han, Cliff, Detter, John C., Übler, Susanne, Rohde, Manfred, Tindall, Brian J., Göker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6(T)). Standards in Genomic Sciences, 4 (2), 131-143. doi: 10.4056/sigs.1463589
Deangelis, Kristen M., Allgaier, Martin, Chavarria, Yaucin, Fortney, Julian L., Hugenholtz, Philip, Simmons, Blake, Sublette, Kerry, Silver, Whendee L. and Hazen, Terry C. (2011). Characterization of trapped lignin-degrading microbes in tropical forest soil. Plos One, 6 (4) e19306, e19306.1-e19306.9. doi: 10.1371/journal.pone.0019306
Zhang, Tao, Datta, Supratim, Eichler, Jerry, Ivanova, Natalia, Axen, Seth D., Kerfeld, Cheryl A., Chen, Feng, Kyrpides, Nikos, Hugenholtz, Philip, Cheng, Jan-Fang, Sale, Kenneth L., Simmons, Blake and Rubin, Eddy (2011). Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chemistry, 13 (8), 2083-2090. doi: 10.1039/c1gc15193b
Goker, Markus, Cleland, David, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Beck, Brian, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Klenk, Hans-Peter (2011). Complete genome sequence of Isosphaera pallida type strain (IS1BT). Standards in Genomic Sciences, 4 (1), 63-71. doi: 10.4056/sigs.1533840
Gronow, Sabine, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynn, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, Manfred, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T). Standards in Genomic Sciences, 4 (1), 36-44. doi: 10.4056/sigs.1503846
Pitluck, Sam, Sikorski, Johannes, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Djao, Oliver D. Ngatchou, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja ... Land, Miriam (2011). Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1 T). Standards in Genomic Sciences, 4 (1), 54-62. doi: 10.4056/sigs.1523807
Pagani, Ioanna, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Desh-Pande, Shweta, Cheng, Jan-Fang, Chertkov, Olga, Davenport, Karen, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Kannan, K. Palani, Djao, Olivier D. Ngatchou, Rohde, Manfred ... Klenk, Hans-Peter (2011). Complete genome sequence of Desulfobulbus propionicus type strain (1pr3 T). Standards in Genomic Sciences, 4 (1), 100-110. doi: 10.4056/sigs.1613929
Abt, Birte, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Tindall, Brian J., Detter, John C., Woyke, Tanja, Bristow, James ... Kyrpides, Nikos C. (2011). Complete genome sequence of leadbetterella byssophila type strain (4M15 T). Standards in Genomic Sciences, 4 (1), 2-12. doi: 10.4056/sigs.1413518
Chertkov, Olga, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Djao, Oliver D. N., Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Han, Cliff, Detter, John C., Rohde, Manfred, Goker, Markus, Woyke, Tanja ... Kyrpides, Nikos C. (2011). Complete genome sequence of Thermomonospora curvata type strain (B9 T). Standards in Genomic Sciences, 4 (1), 13-22. doi: 10.4056/sigs.1453580
Lang, Elke, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Kopitz, Markus, Rohde, Manfred, Goker, Markus, Tindall, Brian J. ... Kyrpides, Nikos C. (2011). Complete genome sequence of Weeksella virosa type strain (9751 T). Standards in Genomic Sciences, 4 (1), 81-90. doi: 10.4056/sigs.1603927
Ivanova, Natalia, Rohde, Christine, Munk, Christine, Nolan, Matt, Lucas, Susan, del Rio,Tijana Glavina, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck. Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Mikhailova,Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, , Manfred, Goker, Markus, Tindall, Brian J., Woyke, Tanja, Bristow, James ... Lapidus,Alla (2011). Complete genome sequence of Truepera radiovictrix type strain (RQ-24 T). Standards in Genomic Sciences, 4 (1), 91-96. doi: 10.4056/sigs.1563919
Klenk, Hans-Peter, Lapidus, Alla, Chertkov, Olga, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Daum, Chris, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Abt, Birte, Pukall, Rüdiger, Göker, Markus ... Eisen, Jonathan A. (2011). Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Ra. Standards in Genomic Sciences, 5 (1), 121-134. doi: 10.4056/sigs.2144922
Goker, Markus, Daligault, Hajnalka, Mwirichia, Romano, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Han, Cliff, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Wirth, Reinhard, Detter, John C., Woyke, Tanja ... Klenk, Hans-Peter (2011). Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Standards in Genomic Sciences, 5 (3), 407-415. doi: 10.4056/sigs.2465574
Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Chertkov, Olga, Del Rio, Tijana Galvina, Nolan, Matt, Copeland, Alex, Tice, Hope, Cheng, Jan-Feng, Lucas, Susan, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Mavromatis, Konstantinos, Liolios, Konstantinos, Brettin, Thomas, Fiebig, Anne, Rohde, Manfred, Abt, Birte, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2011). Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T)). Standards in Genomic Sciences, 5 (1), 97-111. doi: 10.4056/sigs.2114901
Lapidus, Alla, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Abt, Birte, Spring, Stefan, Goker, Markus, Bristow, James, Eisen, Jonathan A. ... Woyke, Tanja (2011). Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10(T)). Standards in Genomic Sciences, 5 (1), 86-96. doi: 10.4056/sigs.2235024
Pati, Amrita, Gronow, Sabine, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Mikhailova, N, Huntemann, Marcel, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Ivanova, Natalia (2011). Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20(T)). Standards in Genomic Sciences, 5 (1), 41-49. doi: 10.4056/sigs.2164949
Liolios, Konstantinos, Sikorski, Johannes, Lu, Meagan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kotsyurbenko, Oleg, Rohde, Manfred, Tindall, Brian J., Abt, Birte, Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113(T)). Standards in Genomic Sciences, 5 (1), 30-40. doi: 10.4056/sigs.2154937
Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262(T)). Standards in Genomic Sciences, 5 (1), 21-29. doi: 10.4056/sigs.2124912
Goker, Markus, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2011). Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T)). Standards in Genomic Sciences, 4 (3), 393-401. doi: 10.4056/sigs.2064705
Anderson, Iain, Goker, Markus, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Huber, Harald, Yasawong, Montri, Rohde, Manfred, Spring, Stefan, Abt, Birte, Sikorski, Johannes ... Lapidus, Alla (2011). Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T)). Standards in Genomic Sciences, 4 (3), 381-392. doi: 10.4056/sigs.2014648
Han, Cliffe, Mwirichia, Romano, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus ... Detter, John C. (2011). Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR(T)). Standards in Genomic Sciences, 4 (3), 371-380. doi: 10.4056/sigs.2004684
Han, Cliff, Gronow, Sabine, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Zeytun, Ahmed, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James ... Detter, John C. (2011). Complete genome sequence of Treponema succinifaciens type strain (6091(T)). Standards in Genomic Sciences, 4 (3), 361-370. doi: 10.4056/sigs.1984594
Daligault, Hajnalka, Lapidus, Alla, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Galvina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Verbarg, Susanne, Goker, Markus, Bristow, James, Eisen, JA ... Woyke, Tanja (2011). Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T). Standards in Genomic Sciences, 4 (3), 352-360. doi: 10.4056/sigs.1964579
Munk, A. Christine, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Del Rio, Tijana Glavina, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Huntemann, Marcel, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Tapia, Roxanne, Han, Cliff, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Yasawong, Montri, Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Goker, Markus ... Klenk, Hans-Peter (2011). Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T)). Standards in Genomic Sciences, 4 (3), 342-351. doi: 10.4056/sigs.1894556
Sikorski, Johannes, Teshima, Hazuki, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Ngatchou-Djao, Oliver Duplex, Rohde, Manfred, Pukall, Rudiger, Spring, Stefan, Abt, Birte, Goker, Markus, Detter, John C. ... Lapidus, Alla (2011). Complete genome sequence of mahella australiensis type strain (50-1 BONT). Standards in Genomic Sciences, 4 (3), 331-341. doi: 10.4056/sigs.1864526
Anderson, Iain, Sikorski, Johannes, Zeytun, Ahmet, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Ngatchou-Djao, Oliver D., Rohde, Manfred, Tindall, Brian J., Goker, Markus ... Kyrpides, Nikos C. (2011). Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1(T)). Standards in Genomic Sciences, 4 (3), 322-330. doi: 10.4056/sigs.1844518
Ivanova, Natalia, Sikorski, Johannes, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Tindall, Brian J., Goker, Markus, Detter, John C., Woyke, Tanja ... Lapidus, Alla (2011). Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL(T)). Standards in Genomic Sciences, 4 (3), 312-321. doi: 10.4056/sigs.1824509
Huntemann, Marcel, Lu, Megan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelynne-Marie, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja, Bristow, James ... Mavromatis, Konstantinos (2011). Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T). Standards in Genomic Sciences, 4 (3), 303-311. doi: 10.4056/sigs.1814460
Lykidis, Athanasios, Chen, Chia-Lung, Tringe, Susannah G., McHardy, Alice C., Copeland, Alex, Kyrpides, Nikos C., Hugenholtz, Philip, Macarie, Hervé, Olmos, Alejandro, Monroy, Oscar and Liu, Wen-Tso (2011). Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME Journal, 5 (1), 122-130. doi: 10.1038/ismej.2010.125
Burnum, Kristin E., Callister, Stephen J., Nicora, Carrie D., Purvine, Samuel O., Hugenholtz, Philip, Warnecke, Falk, Scheffrahn. Rudolf H., Smith, Richard D. and Lipton, Mary S. (2011). Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME Journal, 5 (1), 161-164. doi: 10.1038/ismej.2010.97
Pati, Amrita, Gronow, Sabine, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lucas, Susan (2011). Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T). Standards in Genomic Sciences, 4 (1), 45-53. doi: 10.4056/sigs.1513795
Abt, Birte, Lu, Megan, Misra, Monica, Han, Cliff, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Rohde, Manfred, Tindall, Brian J., Goeker, Markus ... Lapidus, Alla (2011). Complete genome sequence of Cellulophaga algicola type strain (IC166(T)). Standards in Genomic Sciences, 4 (1), 72-80. doi: 10.4056/sigs.1543845
Sikorski, Johannes, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Yasawong, Montri, Rohde, Manfred, Pukall, Ruediger, Spring, Stefan, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1(T)). Standards in Genomic Sciences, 3 (3), 304-314. doi: 10.4056/sigs.1273360
Pitluck, Sam, Yasawong, Montri, Held, Brittany, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Goodwin, Lynne, Tapia, Roxane, Han, Cliff, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pukall, Ruediger, Spring, Stefan, Rohde, Manfred, Sikorski, Johannes ... Klenk, Hans-Peter (2010). Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3(T)). Standards in Genomic Sciences, 3 (3), 285-293. doi: 10.4056/sigs.1253298
Sun, Hui, Spring, Stefan, Lapidus, Alla, Davenport, Karen, Del Rio, Tijana Glavina, Tice, Hope, Nolan, Matt, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Pagani, Ionna, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Han, Cliff, Rohde, Manfred, Brambilla, Evelyne, Goeker, Markus, Woyke, Tanja ... Land, Miriam (2010). Complete genome sequence of Desulfarculus baarsii type strain (2st14(T)). Standards in Genomic Sciences, 3 (3), 276-284. doi: 10.4056/sigs.1243258
Yilmaz, S, Allgaier, M and Hugenholtz, P (2010). Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods, 7 (12), 943-944. doi: 10.1038/nmeth1210-943
Clum, Alicia, Tindall, Brian J., Sikorski, Johannes, Ivanova, Natalia, Mavromatis, Konstantinos, Lucas, Susan, Glavina Del Rio, Tijana, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Thomas, Brettin, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miram, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick ... Lapidus, Alla (2010). Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377 T). Standards in Genomic Sciences, 2 (2), 228-228. doi: 10.4056/sigs.88.1234
Saunders, Elisabeth, Tindall, Brian J., Fähnrich, Regine, Lapidus, Alla, Copeland, Alex, del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Göker, Markus, Bristow, James ... Kyrpides, Nikos C. (2010). Complete genome sequence of Haloterrigena turkmenica type strain (4k T). Standards in Genomic Sciences, 2 (1), 107-116. doi: 10.4056/sigs.681272
Anderson, Iain, Djao, Olivier Duplex, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Giavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han. Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences, 3 (3), 315-324. doi: 10.4056/sigs.1283367
Ochman, Howard, Worobey, Michael, Kuo, Chih-Horng, Ndjango, Jean-Bosco N., Peeters, Jean-Bosco N., Hahn, Beatrice H. and Hugenholtz, Philip (2010). Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology, 8 (11 Article number e1000546) e1000546, e1000546. doi: 10.1371/journal.pbio.1000546
Brambilla, Evelyne, Djao, Olivier Duplex, Daligault, Hajnalka, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Nolan , Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences, 3 (2), 203-211. doi: 10.4056/sigs.1183143
Pitluck, Sam, Yasawong, Montri, Munk, Christine, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P(T)). Standards in Genomic Sciences, 3 (2), 108-116. doi: 10.4056/sigs.1133078
Yilmaz, S, Haroon, MF, Rabkin, BA, Tyson, GW and Hugenholtz, P (2010). Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal, 4 (10), 1352-1356. doi: 10.1038/ismej.2010.73
He, Shaomei, Wurtzel, Omri, Singh, Kanwar, Froula, Jeff L., Yilmaz, Suzan, Tringe, Susannah G., Wang, Zhong, Chen, Feng, Lindquist, Erika A., Sorek, Rotem and Hugenholtz, Philip (2010). Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nature Methods, 7 (10), 807-812. doi: 10.1038/NMETH.1507
Goeker, Markus, Held, Brittany, Lucas, Susan, Nolan, Matt, Yasawong, Montri, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, John C., Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Woyke, Tanja ... Lapidus, Alla (2010). Complete genome sequence of Olsenella uli type strain (VPI D76D-27C(T)). Standards in Genomic Sciences, 3 (1), 76-84. doi: 10.4056/sigs.1082860
Pope, P. B., Denman, S. E., Jones, M., Tringe, S. G., Barry, K., Malfatti, S. A., McHardy, A. C., Cheng, J. F., Hugenholtz, P., McSweeney, C. S. and Morrison, M. (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proceedings of the National Academy of Sciences of the United States of America, 107 (33), 14793-1-14798-6. doi: 10.1073/pnas.1005297107
Chang, Yun-Juan, Pukall, Rüdiger, Saunders, Elizabeth, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Glavina Del Rio, Tijana, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han. Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Liolios, Konstantinos, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Goker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Standards in Genomic Sciences, 3 (1), 1-14. doi: 10.4056/sigs.1002553
Abt, Birte, Foster, Brian, Lapidus, Alla, Clum, Alicia, Sun, Hui, Pukall, Rüdiger, Lucas, Susan, Giavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Elsen, Jonathan A. ... Klenk, Hans-Peter (2010). Complete genome sequence of Cellulomonas flavigena type strain (134). Standards in Genomic Sciences, 3 (1), 15-25. doi: 10.4056/sigs.1012662
Ivanova, Natalia, Tringe, Susannah G., Liolios, Konstantinos, Liu, Wen-Tso, Morrison, Norman, Hugenholtz, Philip and Kyrpides, Nikos C. (2010). A call for standardized classification of metagenome projects. Environmental Microbiology, 12 (7), 1803-1805. doi: 10.1111/j.1462-2920.2010.02270.x
Chertkov, Olga, Sikorski, Johannes, Brambilla, Evelyne, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Spring, Stefan, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Standards in Genomic Sciences, 2 (3), 280-289. doi: 10.4056/sigs.902116
von Jan, Mathias, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Goodwin, Lynne, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Chertkov, Olga, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Chain, Patrick, Eichinger, Konrad ... Klenk, Hans-Peter (2010). Complete genome sequence of Archaeoglobus profundus type strain (AV18(T)). Standards in Genomic Sciences, 2 (3), 327-346. doi: 10.4056/sigs.942153
Liolios, Konstantinos, Sikorski, Johannes, Jando, Marlen, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Woyke, Tanja, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chertkov, Olga, Kuske, Cheryl, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus ... Kyrpides, Nikos C. (2010). Complete genome sequence of Thermobispora bispora type strain (R51(T)). Standards in Genomic Sciences, 2 (3), 318-326. doi: 10.4056/sigs.962171
Pati, Amrita, Sikorski, Johannes, Gronow, Sabine, Munk, Christine, Lapidus, Alla, Copeland, Alex, Del Tio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Spring, Stefan ... Klenk, Hans-Peter (2010). Complete genome sequence of Brachyspira murdochii type strain (56-150(T)). Standards in Genomic Sciences, 2 (3), 260-269. doi: 10.4056/sigs.831993
Spring, Stefan, Rachel, Reinhard, Lapidus, Alla, Davenport, Karen, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Brettin, Thomas, Detter, John C., Tapia, Roxanne, Han, Cliff, Heimerl, Thomas, Weikl, Fabian ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermosphaera aggregans type strain (M11TL(T)). Standards in Genomic Sciences, 2 (3), 245-259. doi: 10.4056/sigs.821804
DeAngelis, Kristen M., Gladden, John M., Allgaier, Martin, D'haeseleer, Patrik, Fortney, Julian L., Reddy, Amitha, Hugenholtz, Philip, Singer, Steven W., Vander Gheynst, Jean S., Silver, Whendee L., Simmons, Blake A. and Hazen, Terry C. (2010). Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities. BioEnergy Research, 3 (2), 146-158. doi: 10.1007/s12155-010-9089-z
He, Shaomei, Kunin, Victor, Haynes, Matthew, Martin, Hector Garcia, Ivanova, Natalia, Rohwer, Forest, Hugenholtz, Philip and McMahon, Katherine D. (2010). Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environmental Microbiology, 12 (5), 1205-1217. doi: 10.1111/j.1462-2920.2010.02163.x
Engelbrektson, Anna, Kunin, Victor, Wrighton, Kelly C., Zvenigorodsky, Natasha, Chen, Feng, Ochman, Howard and Hugenholtz, Philip (2010). Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME Journal, 4 (5), 642-647. doi: 10.1038/ismej.2009.153
Tice, Hope, Mayilraj, Shanmugam, Sims, David, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Copeland, Alex, Cheng, Jan-Fang, Meincke, Linda, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Chen, Feng (2010). Complete genome sequence of Nakamurella multipartita type strain (Y-104(T)). Standards in Genomic Sciences, 2 (2), 168-175. doi: 10.4056/sigs.721316
Harmon-Smith, Miranda, Celia, Laura, Chertkov, Olga, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Goeker, Markus, Beck, Brian ... Chen, Feng (2010). Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300(T)). Standards in Genomic Sciences, 2 (2), 220-227. doi: 10.4056/sigs.811799
Sikorski, Johannes, Lapidus, Alla, Copeland, Alex, Misra, Monica, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Jando, Marlen, Schneider, Susanne, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chertkov, Olga, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C. ... Klenk, Hans-Peter (2010). Complete genome sequence of Segniliparus rotundus type strain (CDC 1076(T)). Standards in Genomic Sciences, 2 (2), 203-211. doi: 10.4056/sigs.791633
Lail, Kathleen, Sikorski, Johannes, Saunders, Elizabeth, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Brettin, Thomas, Detter, John C., Schuetze, Andrea, Rohde, Manfred, Tindall, Brian J. ... Chen, Feng (2010). Complete genome sequence of Spirosoma linguale type strain (1(T)). Standards in Genomic Sciences, 2 (2), 176-185. doi: 10.4056/sigs.741334
Foster, Brian, Pukall, Ruediger, Abt, Birte, Nolan, Matt, Del Rio, Tijana Glavina, Chen, Feng, Lucas, Susan, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Rohde, Manfred, Goeker, Markus ... Lapidus, Alla (2010). Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07(T)). Standards in Genomic Sciences, 2 (1), 1-8. doi: 10.4056/sigs.571102
Mavromatis, Konstantinos, Sikorski, Johannes, Pabst, Elke, Teshima, Hazuki, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Goeker, Markus, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Vulcanisaeta distributa type strain (IC-017(T)). Standards in Genomic Sciences, 3 (2), 117-125. doi: 10.4056/sigs.1113067
Allagier, Martin, Reddy, Amitha, Park, Joshua I., Ivanova, Natalia, D'haeseleer, Patrik, Lowry, Steve, Sapra, Rajat, Hazen, Terry C., Simmons, Blake A., VanderGheynst, Jean S. and Hugenholtz, Philip (2010). Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One, 5 (1) e8812, e8812-1-e8812-9. doi: 10.1371/journal.pone.0008812
Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Goker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea- An International Microbiological Journal, 2010 690737, 1-16. doi: 10.1155/2010/690737
Del Rio, Tijana Glavina, Chertkov, Olga, Yasawong, Montri, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Pukall, Ruediger, Sikorski, Johannes, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Lapidus, Alla (2010). Complete genome sequence of Intrasporangium calvum type strain (7 KIPT). Standards in Genomic Sciences, 3 (3), 294-303. doi: 10.4056/sigs.1263355
Sikorski, Johannes, Munk, Christine, Lapidus, Alla, Djao, Olivier Duplex Ngatchou, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Sims, David, Meincke, Linda, Brettin, Thomas, Detter, John C., Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Sulfurimonas autotrophica type strain (OK10(T)). Standards in Genomic Sciences, 3 (2), 194-202. doi: 10.4056/sigs.1173118
Yasawong, Montri, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Arcanobacterium haemolyticum type strain (11018(T)). Standards in Genomic Sciences, 3 (2), 126-135. doi: 10.4056/sigs.1123072
Mavromatis, Konstantinos, Yasawong, Montri, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Tapia, Roxanne, Han, Cliff, Bruce, David, Goodwin, Lynne, Pati, Amrita, Chen, Ami, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Brambilla, Evelyne, Spring, Stefan, Goeker, Markus, Sikorski, Johannes ... Kyrpides, Nikos C. (2010). Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T)). Standards in Genomic Sciences, 3 (2), 136-144. doi: 10.4056/sigs.1143106
LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2010). Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T)). Standards in Genomic Sciences, 3 (1), 85-92. doi: 10.4056/sigs.1092865
Sikorski, Johannes, Lapidus, Alla, Chertkov, Olga, Lucas, Susan, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Brambilla, Evelyne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Bruce, David, Detter, Chris, Tapia, Roxanne, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T)). Standards in Genomic Sciences, 3 (1), 57-65. doi: 10.4056/sigs.1062906
Goeker, Markus, Held, Brittany, Lapidus, Alla, Nolan, Matt, Spring, Stefan, Yasawong, Montri, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Tapia, Roxanne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Brambilla, Evelyne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1(T)). Standards in Genomic Sciences, 3 (1), 66-75. doi: 10.4056/sigs.1072907
Tindall, Brian J., Sikorski, Johannes, Lucas, Susan, Goltsman, Eugene, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Faehnrich, Regine, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Lapidus, Alla (2010). Complete genome sequence of Meiothermus ruber type strain (21(T)). Standards in Genomic Sciences, 3 (1), 26-36. doi: 10.4056/sigs.1032748
Sikorski, Johannes, Tindall, Brian J., Lowry, Stephen, Lucas, Susan, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Lapidus, Alla (2010). Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T)). Standards in Genomic Sciences, 3 (1), 37-46. doi: 10.4056/sigs.1042812
LaButti, Kurt, Sikorski, Johannes, Schneider, Susanne, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Tindall, Brian J., Rohde, Manfred, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2010). Complete genome sequence of Planctomyces limnophilus type strain (Mu 290(T)). Standards in Genomic Sciences, 3 (1), 47-56. doi: 10.4056/sigs.1052813
Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Ruediger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Detter, John C. (2010). Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009). Standards in Genomic Sciences, 2 (3), 361-362. doi: 10.4056/sigs.992408
Kiss, Hajnalka, Lang, Elke, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Del Rio, Tijana Glavina, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Spring, Stefan, Rohde, Manfred, Goeker, Markus, Woyke, Tanja ... Klenk, Hans-Peter (2010). Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460(T)). Standards in Genomic Sciences, 2 (3), 270-279. doi: 10.4056/sigs.892105
Mavromatis, Konstantinos, Abt, Birte, Brambilla, Evelyne, Lapidus, Alla, Copeland, Alex, Deshpande, Shweta, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Woyke, Tanja, Goodwin, Lynne, Pitluck, Sam, Held, Brittany, Brettin, Thomas, Tapia, Roxanne, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Liolios, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24(T)). Standards in Genomic Sciences, 2 (3), 290-299. doi: 10.4056/sigs.952166
Wirth, Reinhard, Sikorski, Johannes, Brambilla, Evelyne, Misra, Monica, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Tapia, Roxane, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Anderson, Iain, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Bilek, Yvonne, Hader, Thomas, Land, Miriam, Hauser, Loren, Chang, Yun-Juan ... Klenk, Hans-Peter (2010). Complete genome sequence of Thermocrinis albus type strain (HI 11/12(T)). Standards in Genomic Sciences, 2 (2), 194-202. doi: 10.4056/sigs.761490
Pukall, Ruediger, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C., Rohde, Manfred, Goeker, Markus ... Hugenholtz, Philip (2010). Complete genome sequence of Conexibacter woesei type strain (ID131577(T)). Standards in Genomic Sciences, 2 (2), 212-219. doi: 10.4056/sigs.751339
Pukall, Ruediger, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, LaButti, Kurt, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor ... Brettin, Thomas (2010). Complete genome sequence of Kribbella flavida type strain (IFO 14399(T)). Standards in Genomic Sciences, 2 (2), 186-193. doi: 10.4056/sigs.731321
Ivanova, Natalia, Sikorski, Johannes, Jando, Marlen, Munk, Christine, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Meincke, Linda, Brettin, Thomas, Detter, John C., Rohde, Manfred, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Geodermatophilus obscurus type strain (G-20(T)). Standards in Genomic Sciences, 2 (2), 158-167. doi: 10.4056/sigs.711311
Sikorski, Johannes, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Rohde, Manfred, Lang, Elke ... Klenk, Hans-Peter (2010). Complete genome sequence of Sulfurospirillum deleyianum type strain (5175(T)). Standards in Genomic Sciences, 2 (2), 149-157. doi: 10.4056/sigs.671209
Saunders, Elisabeth, Tindall, Brian J., Faehnrich, Regine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, James ... Kyrpides, Nikos C. (2010). Complete genome sequence of Haloterrigena turkmenica type strain (4k(T)). Standards in Genomic Sciences, 2 (1), 107-116. doi: 10.4056/sigs.68923
Ivanova, Natalia, Daum, Chris, Lang, Elke, Abt, Birte, Kopitz, Markus, Saunders, Elizabeth, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brettin, Thomas, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Haliangium ochraceum type strain (SMP-2(T)). Standards in Genomic Sciences, 2 (1), 96-106. doi: 10.4056/sigs.69.1277
Gronow, Sabine, Welnitz, Sabine, Lapidus, Alla, Nolan, Matt, Ivanova, Natalia, Del Rio, Tijana Glavina, Copeland, Alex, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Saunders, Elizabeth, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Goeker, Markus ... Lucas, Susan (2010). Complete genome sequence of Veillonella parvula type strain (Te3(T)). Standards in Genomic Sciences, 2 (1), 57-65. doi: 10.4056/sigs.521107
Pati, Amrita, LaButti, Kurt, Pukall, Ruediger, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pitluck, Sam, Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Brettin, Thomas, Sikorski, Johannes, Rohde, Manfred, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Lapidus, Alla (2010). Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022(T)). Standards in Genomic Sciences, 2 (1), 49-56. doi: 10.4056/sigs.601105
Spring, Stefan, Nolan, Matt, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Land, Miriam, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Munk, Christine, Kiss, Hajnalka, Chain, Patrick, Han, Cliff, Brettin, Thomas, Detter, John C., Schueler, Esther ... Klenk, Hans-Peter (2010). Complete genome sequence of Desulfohalobium retbaense type strain (HR100T). Standards in Genomic Sciences, 2 (1), 38-48. doi: 10.4056/sigs.581048
Mavromatis, Konstantinos, Sikorski, Johannes, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Chertkov, Olga, Han, Cliff, Brettin, Thomas, Detter, John C. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T)). Standards in Genomic Sciences, 2 (1), 9-18. doi: 10.4056/sigs.591104
Ivanova, Natalia, Sikorski, Johannes, Jando, Marlen, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Han, Cliff, Detter, John C., Brettin, Thomas, Rohde, Manfred ... Kyrpides, Nikos C. (2010). Complete genome sequence of Gordonia bronchialis type strain (3410(T)). Standards in Genomic Sciences, 2 (1), 19-28. doi: 10.4056/sigs.611106
Nolan, Matt, Sikorski, Johannes, Jando, Marlen, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Sims, David, Meincke, Linda, Brettin, Thomas, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred ... Klenk, Hans-Peter (2010). Complete genome sequence of Streptosporangium roseum type strain (NI 9100(T)). Standards in Genomic Sciences, 2 (1), 29-37. doi: 10.4056/sigs.631049
Pati, Amrita, Gronow, Sabine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Chertkov, Olga, Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Goeker, Markus, Bristow, James, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2010). Complete genome sequence of Arcobacter nitrofigilis type strain (CIT). Standards in Genomic Sciences, 2 (3), 300-308. doi: 10.4056/sigs.912121
Djao, Olivier Duplex Ngatchou, Zhang, Xiaojing, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Sikorski, Johannes, Spring, Stefan, Goeker, Markus ... Klenk, Hans-Peter (2010). Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1(T)). Standards in Genomic Sciences, 3 (3), 267-275. doi: 10.4056/sigs.1233249
Han, Cliff, Gu, Wei, Zhang, Xiaojing, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Goodwin, Lynne, Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Schneider, Susanne, Rohde, Manfred, Goeker, Markus, Pukall, Ruediger, Woyke, Tanja ... Detter, John C. (2010). Complete genome sequence of Thermaerobacter marianensis type strain (7p75a(T)). Standards in Genomic Sciences, 3 (3), 337-345. doi: 10.4056/sigs.1373474
Sun, Hui, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Djao, Olivier Duplex Ngatchou, Rohde, Manfred, Sikorski, Johannes, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Klenk, Hans-Peter (2010). Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509(T)). Standards in Genomic Sciences, 3 (3), 325-336. doi: 10.4056/sigs.1363462
Del Rio, Tijana Glavina, Abt, Birte, Spring, Stefan, Lapidus, Alla, Nolan, Matt, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Detter, John C., Brettin, Thomas, Rohde, Manfred, Goeker, Markus, Bristow, Jim ... Lucas, Susan (2010). Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034(T)). Standards in Genomic Sciences, 2 (1), 87-95. doi: 10.4056/sigs.661199
Nolan, Matt, Sikorski, Johannes, Davenport, Karen, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Tapia, Roxanne, Brettin, Thomas, Detter, John C., Han, Cliff, Yasawong, Montri, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja ... Lapidus, Alla (2010). Complete genome sequence of Ferrimonas balearica type strain (PAT(T)). Standards in Genomic Sciences, 3 (2), 174-182. doi: 10.4056/sigs.1161239
Kiss, Hajnalka, Cleland, David, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Lu, Megan, Brettin, Thomas, Detter, John C., Goeker, Markus, Tindall, Brian J., Beck, Brian, McDermott, Timothy R., Woyke, Tanja ... Cheng, Jan-Fang (2010). Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1(T)). Standards in Genomic Sciences, 3 (2), 153-162. doi: 10.4056/sigs.1153107
Wu, Dongying, Hugenholtz, Philip, Mavromatis, Konstantinos, Pukall, Ru¨diger, Dalin, Eileen, Ivanova, Natalia N., Kunin, Victor, Goodwin, Lynne, Wu, Martin, Tindall, Brian J., Hooper, Sean D., Pati, Amrita, Lykidis, Athanasios, Spring, Stefan, Anderson, Iain J., D'haeseleer, Patrik, Zemla, Adam, Singer, Mitchell, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Han, Cliff, Chen, Feng, Cheng, Jan-Fang, Lucas, Susan, Kerfeld, Cheryl, Lang, Elke, Gronow, Sabine, Chain, Patrick ... Elsen, Jonathan A. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462 (7276), 1056-1060. doi: 10.1038/nature08656
Copeland, Alex, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Pukall, Rüdiger, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Detter, John C. (2009). Complete genome sequence of Atopobium parvulum type strain (IPP 1246 T). Standards in Genomic Sciences, 1 (2), 166-173. doi: 10.4056/sigs.29547
Labutti, Kurt, Pukall, Rüdiger, Steenblock, Katja, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Göker, Markus ... Lapidus, Alla (2009). Complete genome sequence of anaerococcus prevotii type strain (PC1 T). Standards in Genomic Sciences, 1 (2), 159-165. doi: 10.4056/sigs.24194
Han, Cliff, Spring, Stefan, Lapidus, Alla, del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Göker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3 T). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4056/sigs.22138
Nolan, Matt, Tindall, Brian J., Pomrenke, Helga, Lapidus, Alla, Copeland, Alex, del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Han, Cliff, Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Ovchinikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Göker, Markus, Bristow, James ... Detter, John C. (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10 T). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs.46736
Liolios, Konstantinos, Chen, I-Min A., Mavromatis, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Markowitz, Victor M. and Kyrpides, Nikos C. (2009). The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research, 38 (Supp. 1) gkp848, D346-D354. doi: 10.1093/nar/gkp848
Kristiansson, Erik, Hugenholtz, Philip and Dalevi, Daniel (2009). ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics, 25 (20), 2737-2738. doi: 10.1093/bioinformatics/btp508
Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V. ... Detter, J. C. (2009). Genome project standards in a new era of sequencing. Science, 326 (5950), 236-237. doi: 10.1126/science.1180614
Kunin, Victor, Engelbrekston, Anna, Ochman, Howard and Hugenholtz, Philip (2009). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12 (1), 118-123. doi: 10.1111/j.1462-2920.2009.02051.x
Hugenholtz, P, Hooper, SD and Kyrpides, NC (2009). Focus: Synergistetes. Environmental Microbiology, 11 (6), 1327-1329. doi: 10.1111/j.1462-2920.2009.01949.x
Herlemann, D. P. R., Geissinger, O., Ikeda-Ohtsubo, W., Kunin, V., Sun, H., Lapidus, A., Hugenholtz, P. and Brune, A. (2009). Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Applied and Environmental Microbiology, 75 (9), 2841-2849. doi: 10.1128/AEM.02698-08
Tschop, MH, Hugenholtz, P and Karp, CL (2009). Getting to the core of the gut microbiome. Nature Biotechnology, 27 (4), 344-346. doi: 10.1038/nbt0409-344
Hugenholtz, P and Kyrpides, NC (2009). A changing of the guard: Genomics update. Environmental Microbiology, 11 (3), 551-553. doi: 10.1111/j.1462-2920.2009.01888.x
Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat and Kyrpides, Nikos C. (2009). Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One, 4 (1) e4192, e4192.1-e4192.8. doi: 10.1371/journal.pone.0004192
Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Schneider, Susanne, Goker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Kytococcus sedentarius type strain (541(T)). Standards in Genomic Sciences, 1 (1), 12-20. doi: 10.4056/sigs.761
Knierim, B., Webb, R., Wilmes, P., Hugenholtz, P., Liphardt, J., McDonald, K., Banfield, J. and Auer, M. (2009). Correlative tem and fish imaging of microbial communities. Microscopy and Microanalysis, 15 (Suppl. 2), 834-835. doi: 10.1017/S1431927609098250
Munk, Chris, Lapidus, Alla, Copeland, Alex, Jando, Marlen, Mayilraj, Shanmugam, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Chain, Patrick, Pitluck, Sam, Goeker, Markus, Ovchinikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21(T)). Standards in Genomic Sciences, 1 (3), 292-299. doi: 10.4056/sigs.47643
Nolan, Matt, Gronow, Sabine, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Sims, David, Meincke, Linda, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Han, Cliff, Detter, John C., Ovchinikova, Galina, Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Chain, Patrick (2009). Complete genome sequence of Streptobacillus moniliformis type strain (9901(T)). Standards in Genomic Sciences, 1 (3), 300-307. doi: 10.4056/sigs.48727
Nolan, Matt, Gronow, Sabine, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex, Lucas, Susan, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Sims, David, Meincke, Linda, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Han, Cliff, Detter, John C., Ovchinikova, Galina, Pati, Amrita, Mavromatis, Konstantinos, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred ... Chain, Patrick (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10(T)). Standards in Genomic Sciences, 1 (3), 283-291. doi: 10.4056/sigs46736
Pukall, Ruedieger, Gehrich-Schroeter, Gabriele, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Copeland, Alex, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Bruce, David, Goodwin, Lynne, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Goeker, Markus, Bristow, Jim ... Han, Cliff (2009). Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134(T)). Standards in Genomic Sciences, 1 (3), 262-269. doi: 10.4056/sigs.41646
Chovatia, Mansi, Sikorski, Johannes, Schroeder, Maren, Lapidus, Alla, Nolan, Matt, Tice, Hope, Del Rio, Tijana Glavina, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Detter, John C., Brettin, Thomas, Rohde, Manfred ... Eisen, Jonathan A. (2009). Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883(T)). Standards in Genomic Sciences, 1 (3), 254-261. doi: 10.4056/sigs.40645
Spring, Stefan, Lapidus, Alla, Schroeder, Maren, Gleim, Dorothea, Sims, David, Meincke, Linda, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas ... Han, Cliff (2009). Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575(T)). Standards in Genomic Sciences, 1 (3), 242-252. doi: 10.4056/sigs.39508
Anderson, Iain, Tindall, Brian J., Pomrenke, Helga, Goeker, Markus, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chertkov, Olga, Bruce, David, Brettin, Thomas, Detter, John C., Han, Cliff, Goodwin, Lynne, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Pitluck, Sam, Pati, Amrita, Mavromatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna ... Klenk, Hans-Peter (2009). Complete genome sequence of Halorhabdus utahensis type strain (AX-2(T)). Standards in Genomic Sciences, 1 (3), 218-225. doi: 10.4056/sigs.31864
Saunders, Elizabeth, Pukall, Ruediger, Abt, Birte, Lapidus, Alla, Del Rio, Tijana Glavina, Copeland, Alex, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C. ... Han, Cliff (2009). Complete genome sequence of Eggerthella lenta type strain (VPI 0255(T)). Standards in Genomic Sciences, 1 (2), 174-182. doi: 10.4056/sigs.33592
LaButti, Kurt, Pukall, Ruediger, Steenblock, Katja, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Goeker, Markus ... Lapidus, Alla (2009). Complete genome sequence of Anaerococcus prevotii type strain (PC1(T)). Standards in Genomic Sciences, 1 (2), 159-165. doi: 10.4056/sigs.2494
Malfatti, Stephanie, Tindall, Brian J., Schneider, Susanne, Faehnrich, Regine, Lapidus, Alla, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Anderson, Iain, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Chain, Patrick (2009). Complete genome sequence of Halogeometricum borinquense type strain (PR3(T)). Standards in Genomic Sciences, 1 (2), 150-158. doi: 10.4056/sigs.23264
Lang, Elke, Lapidus, Alla, Chertkov, Olga, Brettin, Thomas, Detter, John C., Han, Cliff, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Kopitz, Marcus, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Dyadobacter fermentans type strain (NS114(T)). Standards in Genomic Sciences, 1 (2), 133-140. doi: 10.4056/sigs.19262
Ivanova, Natalia, Gronow, Sabine, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Rohde, Christine, Goeker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T)). Standards in Genomic Sciences, 1 (2), 126-132. doi: 10.4056/sigs.1854
Pati, Amrita, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Chain, Patrick, D'haeseleer, Patrik, Chen, Amy, Palaniappan, Krishna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Bristow, Jim ... Klenk, Hans-Peter (2009). Complete genome sequence of Saccharomonospora viridis type strain (P101(T)). Standards in Genomic Sciences, 1 (2), 141-149. doi: 10.4056/sigs.20263
Ivanova, Natalia, Sikorski, Johannes, Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goeker, Markus, Pukall, Ruediger ... Kyrpides, Nikos C. (2009). Complete genome sequence of Sanguibacter keddieii type strain (ST-74(T)). Standards in Genomic Sciences, 1 (2), 110-118. doi: 10.4056/sigs16197
Mavrommatis, Konstantinos, Gronow, Sabine, Saunders, Elizabeth, Land, Miriam, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Detter, John C., Han, Cliff, Bristow, James, Goeker, Markus, Rohde, Manfred ... Hugenholtz, Philip (2009). Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Standards in Genomic Sciences, 1 (2), 101-109. doi: 10.4056/sigs.15195
Mavrommatis, Konstantinos, Pukall, Ruediger, Rohde, Christine, Chen, Feng, Sims, David, Brettin, Thomas, Kuske, Cheryl, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, D'haeseleer, Patrik, Goeker, Markus, Bristow, Jim, Eisen, Jonathan A. ... Kyrpides, Nikos C. (2009). Complete genome sequence of Cryptobacterium curtum type strain (12-3(T)). Standards in Genomic Sciences, 1 (2), 93-100. doi: 10.4056/sigs.12260
Copeland, Alex, Spring, Stefan, Goeker, Markus, Schneider, Susanne, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Meincke, Linda, Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff ... Lucas, Susan (2009). Complete genome sequence of Desulfomicrobium baculatum type strain (X-T). Standards in Genomic Sciences, 1 (1), 29-37. doi: 10.4056/sigs.13134
Clum, Alicia, Nolan, Matt, Lang, Elke, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Goeker, Markus, Spring, Stefan, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Lapidus, Alla (2009). Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences, 1 (1), 38-45. doi: 10.4056/sigs.1463
Lapidus, Alla, Pukall, Ruediger, LaButtii, Kurt, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2009). Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10(T)). Standards in Genomic Sciences, 1 (1), 3-11. doi: 10.4056/sigs.492
Copeland, Alex, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chertkov, Olga, Brettin, Thomas, Detter, John C., Han, Cliff, Ali, Zahid, Tindall, Brian J., Goeker, Markus ... Klenk, Hans-Peter (2009). Complete genome sequence of Catenulispora acidiphila type strain (ID 139908(T)). Standards in Genomic Sciences, 1 (2), 119-125. doi: 10.4056/sigs.17259
Land, Miriam, Lapidus, Alla, Mayilraj, Shanmugam, Chen, Feng, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Rohde, Manfred, Goeker, Markus, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick, Tindall, Brian J. ... Klenk, Hans-Peter (2009). Complete genome sequence of Actinosynnema mirum type strain (101(T)). Standards in Genomic Sciences, 1 (1), 46-53. doi: 10.4056/sigs.21137
Han, Cliff, Spring, Stefan, Lapidus, Alla, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia C., Saunders, Elizabeth, Chertkov, Olga, Brettin, Thomas, Goeker, Markus, Rohde, Manfred, Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3(T)). Standards in Genomic Sciences, 1 (1), 54-62. doi: 10.4506/sigs.22138
Tindall, Brian J., Schneider, Susanne, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Saunders, Elizabeth, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Pati, Amrita, Ivanova, Natalia, Mavrommatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Chain, Patrick, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Han, Cliff, Rohde, Manfred, Goeker, Markus ... Detter, John C. (2009). Complete genome sequence of Halomicrobium mukohataei type strain (arg-2(T)). Standards in Genomic Sciences, 1 (3), 270-277. doi: 10.4056/sigs.42644
Pukall, Ruediger, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Del Rio, Tijana Glavina, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Chertkov, Olga, Bruce, David, Goodwin, Lynne, Kuske, Cheryl, Brettin, Thomas, Detter, John C., Han, Cliff, Pitluck, Sam, Pati, Amrita, Mavrommatis, Konstantinos, Ivanova, Natalia, Ovchinnikova, Galina, Chen, Amy, Palaniappan, Krishna, Schneider, Susanne, Rohde, Manfred, Chain, Patrick, D'haeseleer, Patrik, Goeker, Markus, Bristow, James ... Hugenholtz, Philip (2009). Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1(T)). Standards in Genomic Sciences, 1 (3), 234-241. doi: 10.4056/sigs.37633
Han, Cliff, Sikorski, Johannes, Lapidus, Alla, Nolan, Matt, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Copeland, Alex, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick, Saunders, Elizabeth, Brettin, Thomas, Goeker, Markus, Tindall, Brian J., Bristow, Jim ... Detter, John C. (2009). Complete genome sequence of Kangiella koreensis type strain (SW-125(T)). Standards in Genomic Sciences, 1 (3), 226-233. doi: 10.4056/sigs.36635
Land, Miriam, Pukall, Ruediger, Abt, Birte, Goeker, Markus, Rohde, Manfred, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Lucas, Susan, Chen, Feng, Nolan, Matt, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jefferies, Cynthia C., Saunders, Elizabeth, Brettin, Thomas, Detter, John C., Han, Cliff, Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122(T)). Standards in Genomic Sciences, 1 (1), 21-28. doi: 10.4056/sigs.1162
Clum, Alicia, Tindall, Brian J., Sikorski, Johannes, Ivanova, Natalia, Mavrommatis, Konstantinos, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C., Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Chain, Patrick ... Lapidus, Alla (2009). Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T). Standards in Genomic Sciences, 1 (3), 308-316. doi: 10.4056/sigs.51657
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008). A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews, 72 (4), 557-578. doi: 10.1128/MMBR.00009-08
Wrighton, Kelly C., Agbo, Peter, Warnecke, Falk, Weber, Karrie A., Brodie, Eoin L., DeSantis, Todd Z., Hugenholtz, Philip, Andersen, Gary L. and Coates, John D. (2008). A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME Journal, 2 (11), 1146-1156. doi: 10.1038/ismej.2008.48
Tringe, SG and Hugenholtz, P (2008). A renaissance for the pioneering 16S rRNA gene. Current Opinions in Microbiology, 11 (5), 442-446. doi: 10.1016/j.mib.2008.09.011
Peterson, S. Brook, Warnecke, Falk, Madejska, Julita, McMahon, Katherine D. and Hugenholtz, Philip (2008). Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environmental Microbiology, 10 (10), 2692-2703. doi: 10.1111/j.1462-2920.2008.01690.x
Hugenhotz, Philip and Tyson, Gene W. (2008). Microbiology: Metagenomics. Nature, 455 (7212), 481-483. doi: 10.1038/455481a
Lars M. Blank, Philip Hugenholtz and Nielsen, Lars K. (2008). Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci. Journal of Molecular Evolution, 67 (1), 13-22. doi: 10.1007/s00239-008-9117-1
Kunin, Victor, Raes, Jeroen, Harris, J. Kirk, Spear, John R., Walker, Jeffrey J., Ivanova, Natalia, Von Mering, Christian, Bebout, Brad M., Pace, Norman R., Bork, Peer and Hugenholtz, Philip (2008). Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology, 4 (1) 198, 198. doi: 10.1038/msb.2008.35
Elkins, James G., Podar, Mircea, Graham, David E., Makarova, Kira S., Wolf, Yuri, Randau, Lennart, Hedlund, Brian P., Brochier-Armanet, Celine, Kunin, Victor, Anderson, Iain, Lapidus, Alla, Goltsman, Eugene, Barry, Kerrie, Koonin, Eugene V., Hugenholtz, Philip, Kyrpides, Nikos, Wanner, Gerhard, Richardson, Paul, Keller, Martin and Stetter, Karl O. (2008). A korarchaeal genome reveals insights into the evolution of the Archaea. Proceedings of the National Academy of Sciences of the United States of America, 105 (23), 8102-8107. doi: 10.1073/pnas.0801980105
Field, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J., Angiuoli, Samuel V., Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, dePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan ... Wipat, Anil (2008). The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26 (5), 541-547. doi: 10.1038/nbt1360
Sorek, R, Kunin, V and Hugenholtz, P (2008). CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6 (3), 181-186. doi: 10.1038/nrmicro1793
Kunin, V., He, S., Warnecke, F., Peterson, S. B., Martin, H. G., Haynes, M., Ivanova, N., Blackall, L. L., Breitbart, M., Rohwer, F., McMahon, K. D. and Hugenholtz, P. (2008). A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research, 18 (2), 293-297. doi: 10.1101/gr.6835308
Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, Chen, I-Min A., Grechkin, Yuri, Dubchak, Inna, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Hugenholtz, Philip and Kyrpides, Nikos C. (2008). IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Research, 36 (Supp. 1), D534-D538. doi: 10.1093/nar/gkm869
Warnecke, Falk, Luginbuehl, Peter, Ivanova, Natalia, Ghassemian, Majid, Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Sorek, Rotem, Tringe, Susannah G., Podar, Mircea, Martin, Hector Garcia, Kunin, Victor, Dalevi, Daniel, Madejska, Julita, Kirton, Edward, Platt, Darren, Szeto, Ernest, Salamov, Asaf, Barry, Kerrie, Mikhailova, Natalia, Kyrpides, Nikos C., Matson, Eric G., Ottesen, Elizabeth A., Zhang, Xinning, Hernandez, Myriam, Murillo, Catalina ... Leadbetter, Jared R. (2007). Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450 (7169), 560-565. doi: 10.1038/nature06269
Dalevi, Daniel, DeSantis, Todd Z., Fredslund, Jakob, Andersen, Gary L., Markowitz, Victor M. and Hugenholtz, Philip (2007). Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. BMC Bioinformatics, 8 (1) 402. doi: 10.1186/1471-2105-8-402
Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Losekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A. and Quake, Stephen R. (2007). Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America, 104 (29), 11889-11894. doi: 10.1073/pnas.0704662104
Yamada, Takeshi, Yamauchi, Toshihiro, Shiraishi, Koji, Hugenholtz, Philip, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi, Nakamura, Kazunori and Sekiguchi, Yuji (2007). Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. The ISME Journal, 1 (3), 246-255. doi: 10.1038/ismej.2007.28
Hugenholtz, Philip and Ron, Eliora Z. (2007). Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology, 18 (3), 235-236. doi: 10.1016/j.copbio.2007.05.004
Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P. and Bristow, J. (2007). Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology, 45 (6), 1954-1962. doi: 10.1128/JCM.02187-06
Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Michael, Brown, Kyndall, Kyrpides, Nikos C. and Hugenholtz, Philip (2007). CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8 (1) 209, 209-1-209-8. doi: 10.1186/1471-2105-8-209
Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerry, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip and Kyrpides, Nikos C. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4 (6), 495-500. doi: 10.1038/nmeth1043
McMahon, KD, Martin, HG and Hugenholtz, P (2007). Integrating ecology into biotechnology. Current Opinion in Biotechnology, 18 (3), 287-292. doi: 10.1016/j.copbio.2007.04.007
von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N. and Bork, P. (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315 (5815), 1126-1130. doi: 10.1126/science.1133420
Kunin, Victor, Sorek, Rotem and Hugenholtz, Philip (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 (4 Article # R61) R61, R61-1-R61-3. doi: 10.1186/gb-2007-8-4-r61
Warnecke, F and Hugenholtz, P (2007). Building on basic metagenomics with complementary technologies. Genome Biology, 8 (12) 231, 231.1-231.5. doi: 10.1186/gb-2007-8-12-231
McHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007). Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 (1), 63-72. doi: 10.1038/NMETH976
Hugenholtz, Philip (2007). Riding giants. Environmental Microbiology, 9 (1), 5-5. doi: 10.1111/j.1462-2920.2006.01222_4.x
Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 (5807), 1933-1935. doi: 10.1126/science.1132690
Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system (vol 22, pg 359, 2006). Bioinformatics, 22 (20), 2580-2580. doi: 10.1093/bioinformatics/btl436
DeSantis, T. Z., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y. M., Phan, R. and Andersen, G. L. (2006). NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research, 34 (suppl 2), W394-W399. doi: 10.1093/nar/gkl244
Watt, Michelle, Hugenholtz, Philip, White, Rosemary and Vinall, Kerry (2006). Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environmental Microbiology, 8 (5), 871-884. doi: 10.1111/j.1462-2920.2005.00973.x
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, Kimura, Nobutada, Wagner, Michael, Ohashi, Akiyoshi and Harada, Hideki (2006). Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology, 72 (3), 2080-2091. doi: 10.1128/AEM.72.3.2080-2091.2006
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., KELLER, K., Huber, T. L., Dalevi, D., Hu, P. and Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72 (7), 5069-5072. doi: 10.1128/AEM.03006-05
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip and Kyrpides, Nikos C. (2006). The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research, 34 (Supp. 1), D332-D334. doi: 10.1093/nar/gkj145
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, Zhao, Xueling, Dubchak, Inna, Hugenholtz, Philip, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Ivanova, Natalia and Kyrpides, Nikos C. (2006). The integrated microbial genomes (IMG) system. Nucleic Acids Research, 34 (Supp. 1), D344-D348. doi: 10.1093/nar/gkj024
Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf A., Szeto, Ernest, Dalin, Eileen, Putnam, Nik H., Shapiro, Harris J., Pangilinan, Jasmyn L., Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24 (10), 1263-1269. doi: 10.1038/nbt1247
Shah, Nameeta, Teplitsky, Michael V., Minovitsky, Simon, Pennacchio, Len A., Hugenholtz, Philip, Hamann, Bernd and Dubchak, Inna L. (2005). SNP-VISTA: An interactive SNP visualization tool. BMC Bioinformatics, 6 (1) 292. doi: 10.1186/1471-2105-6-292
Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip and Banfield, Jillian F. (2005). Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Applied and Environmental Microbiology, 71 (10), 6319-6324. doi: 10.1128/AEM.71.10.6319-6324.2005
Tringe, Susannah Green, von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., Podar, Mircea, Short, Jay M., Mathur, Eric J., Detter, John C., Bork, Peer, Hugenholtz, Philip and Rubin, Edward M. (2005). Comparative metagenomics of microbial communities. Science, 308 (5721), 554-557. doi: 10.1126/science.1107851
Hugenholtz, Philip and Stackebrandt, Erko (2004). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). International Journal of Systematic and Evolutionary Microbiology, 54 (6), 2049-2051. doi: 10.1099/ijs.0.03028-0
Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip and Janssen, Peter H. (2004). Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Applied and Environmental Microbiology, 70 (10), 5875-5881. doi: 10.1128/AEM.70.10.5875-5881.2004
Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip and Janssen, Peter H. (2004). Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Applied and Environmental Microbiology, 70 (7), 4363-4366. doi: 10.1128/AEM.70.7.4363-4366.2004
Huber, T, Faulkner, G and Hugenholtz, P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20 (14), 2317-2319. doi: 10.1093/bioinformatics/bth226
Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 (6978), 37-43. doi: 10.1038/nature02340
Ginige, MP, Hugenholtz, P, Daims, H, Wagner, M, Keller, J and Blackall, LL (2004). Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied And Environmental Microbiology, 70 (1), 588-596. doi: 10.1128/AEM.70.1.588-596.2004
Joseph, SJ, Hugenholtz, P, Sangwan, P, Osborne, CA and Janssen, PH (2003). Laboratory cultivation of widespread and previously uncultured soil bacteria. Applied and Environmental Microbiology, 69 (12), 7210-7215. doi: 10.1128/AEM.69.12.7210-7215.2003
Baker, BJ, Hugenholtz, P, Dawson, SC and Banfield, JF (2003). Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Applied and Environmental Microbiology, 69 (9), 5512-5518. doi: 10.1128/AEM.69.9.5512-5518.2003
Zhang, H, Sekiguchi, Y, Hanada, S, Hugenholtz, P, Kim, H, Kamagata, Y and Nakamura, K (2003). Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.. International Journal of Systematic and Evolutionary Microbiology, 53 (4), 1155-1163. doi: 10.1099/ijs.0.02520-0
Janssen, PH and Hugenholtz, P (2003). Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae. Archives of Microbiology, 179 (5), 321-328. doi: 10.1007/s00203-003-0528-5
Uzal, FA, Hugenholtz, P, Blackall, LL, Petray, S, Moss, S, Assis, RA, Miyakawa, MF and Carloni, G (2003). PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Veterinary Microbiology, 91 (2-3), 239-248. doi: 10.1016/S0378-1135(02)00291-2
Rossetti, S, Blackall, LL, Majone, M, Hugenholtz, P, Plumb, JJ and Tandoi, V (2003). Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology-sgm, 149 (2), 459-469. doi: 10.1099/mic.0.26018-0
Hugenholtz, P and Huber, T (2003). Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic And Evolutionary Microbiology, 53 (1), 289-293. doi: 10.1099/ijs.0.02441-0
Sait, M, Hugenholtz, P and Janssen, PH (2002). Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environmental Microbiology, 4 (11), 654-666. doi: 10.1046/j.1462-2920.2002.00352.x
Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 (8), 2309-2318. doi: 10.1099/00221287-148-8-2309
Thomsen, TR, Kjellerup, BV, Nielsen, JL, Hugenholtz, P and Nielsen, PH (2002). In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environmental Microbiology, 4 (7), 383-391. doi: 10.1046/j.1462-2920.2002.00316.x
McDevitt, Christopher A., Hugenholtz, Philip, Hanson, Graeme R. and McEwan, Alastair G. (2002). Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Molecular Microbiology, 44 (6), 1575-1587. doi: 10.1046/j.1365-2958.2002.02978.x
Hugenholtz, P (2002). Exploring prokaryotic diversity in the genomic era. Genome Biology, 3 (2) 0003, REVIEWS0003. doi: 10.1186/gb-2002-3-2-reviews0003
Hall, S. J., Hugenholtz, P., Siyambalapitiya, N., Keller, J. and Blackall, L. L. (2002). The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Science And Technology, 46 (1-2), 267-272. doi: 10.2166/wst.2002.0488
McEwan, A. G., Ridge, J. P., McDevitt, C. A. and Hugenholtz, P. (2002). The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements. Geomicrobiology Journal, 19 (1), 3-21. doi: 10.1080/014904502317246138
Hugenholtz, P., Tyson, G. W. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods in molecular biology (Clifton, N.J.), 179, 29-42.
Klein, M., Friedrich, M., Roger, A. J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L. L., Stahl, D. A. and Wagner, M. (2001). Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology, 183 (20), 6028-6035. doi: 10.1128/JB.183.20.6028-6035.2001
Dalevi, D, Hugenholtz, P and Blackall, LL (2001). A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. International Journal of Systematic And Evolutionary Microbiology, 51 (2), 385-391. doi: 10.1099/00207713-51-2-385
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 (1), 411-419. doi: 10.1128/AEM.67.1.411-419.2001
Crocetti, GR, Hugenholtz, P, Bond, PL, Schuler, A, Keller, J, Jenkins, D and Blackall, LL (2000). Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation. Applied and Environmental Microbiology, 66 (3), 1175-1182. doi: 10.1128/AEM.66.3.1175-1182.2000
Fuerst, J. A. and Hugenholtz, P. (2000). Microorganisms should be high on DNA preservation list. Science, 290 (5496), 1503-1503. doi: 10.1126/science.290.5496.1503b
Sandler, S. J., Hugenholtz, P., Schleper, C., DeLong, E. F., Pace, N. R. and Clark, A. J. (1999). Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. Journal of Bacteriology, 181 (3), 907-915.
Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998). Journal of Bacteriology, 180 (24), 6793-6793. doi: 10.1128/jb.180.24.6793-6793.1998
Dojka, M. A., Hugenholtz, P., Haack, S. K. and Pace, N. R. (1998). Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Applied and Environmental Microbiology, 64 (10), 3869-3877.
Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180 (18), 4765-4774.
Hugenholtz, P., Pitulle, C., Hershberger, K. L. and Pace, N. R. (1998). Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology, 180 (2), 366-376.
Blackall, LL, Rossetti, S, Christensson, C, Cunningham, M, Hartman, P, Hugenholtz, P and Tandoi, V (1997). The characterization and description of representatives of 'G' bacteria from activated sludge plants. Letters in Applied Microbiology, 25 (1), 63-69. doi: 10.1046/j.1472-765X.1997.00176.x
Seviour, EM, Blackall, LL, Christensson, C, Hugenholtz, P, Cunningham, MA, Bradford, D, Stratton, HM and Seviour, RJ (1997). The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity. Journal of Applied Microbiology, 82 (4), 411-421. doi: 10.1046/j.1365-2672.1997.00111.x
Fuerst, JA, Gwilliam, HG, Lindsay, M, Lichanska, A, Belcher, C, Vickers, JE and Hugenholtz, P (1997). Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Applied And Environmental Microbiology, 63 (1), 254-262. doi: 10.1128/aem.63.1.254-262.1997
Bradford, D, Hugenholtz, P, Seviour, EM, Cunningham, MA, Stratton, H, Seviour, RJ and Blackall, LL (1996). 16S rRNA analysis of isolates obtained from gram-negative, filamentous bacteria micromanipulated from activated sludge. Systematic and Applied Microbiology, 19 (3), 334-343. doi: 10.1016/S0723-2020(96)80060-9
Hugenholtz, P and Pace, NR (1996). Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends in Biotechnology, 14 (6), 190-197. doi: 10.1016/0167-7799(96)10025-1
Hugenholtz, P, Cunningham, MA, Hendrikz, JK and Fuerst, JA (1995). Desiccation Resistance of Bacteria Isolated From An Air-Handling System Biofilm Determined Using a Simple Quantitative Membrane-Filter Method. Letters in Applied Microbiology, 21 (1), 41-46. doi: 10.1111/j.1472-765X.1995.tb01003.x
Bond, P. L., Hugenholtz, P., Keller, J. and Blackall, L. L. (1995). Bacterial community structures of phosphate-removing and non-phosphate- removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology, 61 (5), 1910-1916. doi: 10.1128/aem.61.5.1910-1916.1995
Blackall, Linda L., Barker, Stephen C. and Hugenholtz, Philip (1995). Phylogenetic Analysis and Taxonomic History of Nocardia pinensis and Nocardia amarae. Systematic and Applied Microbiology, 17 (4), 519-525. doi: 10.1016/S0723-2020(11)80071-8
Blackall, Linda L., Seviour, Elizabeth M., Cunningham, Mitchell A., Seviour, Robert J. and Hugenholtz, Philip (1995). “Microthrix parvicella” is a Novel, Deep Branching Member of the Actinomycetes Subphylum. Systematic and Applied Microbiology, 17 (4), 513-518. doi: 10.1016/S0723-2020(11)80070-6
Yurkov, V, Stackebrandt, E, Holmes, A, Fuerst, JA, Hugenholtz, P, Golecki, J, Gadon, N, Gorlenko, VM, Kompantseva, EI and Drews, G (1994). Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll Alpha-Containing Bacteria and Description of Roseococcus-Thiosulfatophilus Gen-Nov, Sp-Nov, Erythromicrobium-Ramosum Gen-Nov, Sp-Nov, and Erythrobacter-Litoralis Sp-Nov. International Journal of Systematic Bacteriology, 44 (3), 427-434. doi: 10.1099/00207713-44-3-427
Hugenholtz, P, Stackebrandt, E and Fuerst, JA (1994). A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification. Systematic and Applied Microbiology, 17 (1), 51-57. doi: 10.1016/S0723-2020(11)80031-7
Hugenholtz, P and Fuerst, JA (1992). Heterotrophic Bacteria in An Air-Handling System. Applied and Environmental Microbiology, 58 (12), 3914-3920. doi: 10.1128/AEM.58.12.3914-3920.1992
Hugenholtz, P and Macrae, IC (1990). Stimulation of Aldrin and Dieldrin Loss From Soils Treated with Carbon Amendments and Saturated-Ring Analogs. Bulletin of Environmental Contamination and Toxicology, 45 (2), 223-227. doi: 10.1007/BF01700187
Conference Papers
Rehman, S., Budden, K., Quaranta, A., Fuchs, D., Bowerman, K., Vaughan, A., Shukla, S., Brown, A., Alemao, C., Balachandra, L., Gomez, H., Kumar, , Idrees, S., Faiz, A., Hugenholtz, P., Wark, P., Horvat, J., Wood, L., Wheelock, C. and Hansbro, P. (2023). Role of dietary lipids in chronic obstructive pulmonary disease. HOBOKEN: WILEY.
Budden, K., Rehman, S. F., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Alemao, C., Wood, L., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2022). Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models. ERS International Congress 2022, Barcelona, Spain, 4-6 September 2022. Sheffield, United Kingdom: European Respiratory Society. doi: 10.1183/13993003.congress-2022.3289
Henden, Andrea S., Robb, Renee, Forero, Adriana, Kuns, Rachel D., Ensbey, Kathleen S., Chang, Karshing, Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nic, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey (2021). Interferon Lambda Protects Gastrointestinal Stem Cells from Acute Gvhd. 2021 TCT Meetings of ASTCT and CIBMTR, Online, 8-12 February 2021. Amsterdam, Netherlands: Elsevier. doi: 10.1016/s2666-6367(21)00107-x
Rehman, S.F., Bowerman, K.L., Lachner, N., Budden, K.F., Kim, R., Wood, D.L., Gellatly, S.L., Wark, P.A., Hugenholtz, P. and Hansbro, P.M. (2020). Changes in the Gut Microbiome in Chronic Obstructive Pulmonary Disease. American Thoracic Society International Conference 2020, Philadelphia, PA United States, 15-20 May 2020. New York, NY United States: American Thoracic Society. doi: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4473
Cuiv, Paraic O., Krause, Lutz, Wood, David, Hugenholtz, Phil and Tyson, Gene (2020). Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives. FNM 2020 ‐ 4th Meeting of the Federation of Neurogastroenterology and Motility, Adelaide, SA Australia, 25 - 28 March 2020. Chichester, West Sussex United Kingdom: Wiley-Blackwell.
Budden, K., Rehman, Firdous S., Shukla, S., Bowerman, K., Donovan, C., Gomez, H., Sahu, P., Alemao, C., Holmes, A., Dennis, P., Hugenholtz, P., Wark, P. and Hansbro, P. (2020). Diet influences COPD pathogenesis by regulating microbial metabolism. TSANZSRS 2020 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting for Leaders in Lung Health & Respiratory Science, Melbourne, VIC Australia, 27–31 March 2020. Richmond, VIC Australia: Wiley-Blackwell.
Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark and Holtmann, Gerald J. (2020). Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Crohn's and Colitis Congress, Austin, TX, United States, 23-25 January 2020. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(20)32052-7
Tsutsumi, Tamao, Shah, Alok, Lam, Lisa M T, Schlebusch, Sanmarie, Krueger, Annika, Frazer, Ian, Hugenholtz, Phil, Soyer, H Peter, Morrison, Mark, Hill, Michelle, Sedman, Jacqueline and Ismail, Ashraf (2019). 2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study. IDWeek 2019, Washington, DC, United States, 2-6 October 2019. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/ofid/ofz360.1805
Budden, K., Shukla, S., Rehman, Firdous S., Donvan, C., Bowerman, K., Dennis, P., Hugenholtz, P. and Hansbro, P. (2019). Dietary fibre elevates SCFAS and protects against experimental COPD. TSANZSRS 2019 The Australia & New Zealand Society of Respiratory Science and The Thoracic Society of Australia and New Zealand (ANZSRS/TSANZ) Annual Scientific Meeting, Gold Coast, QLD, Australia, 29 March–2 April 2019. Richmond, VIC, Australia : Wiley-Blackwell Publishing Asia. doi: 10.1111/resp.13492
Budden, Kurtis, Shukla, Shakti, Rehman, Saima Firdous, Sahu, Priyanka, Donovan, Chantal, Bowerman, Kate L., Dennis, Paul G., Hugenholtz, Philip and Hansbro, Philip M. (2019). The Role of the Gastrointestinal Microbiome in Lung Cancer Pathogenesis. 2019 Hunter Cancer Research Symposium, Newcastle, NSW Australia, 8 November 2019. Chichester, West Sussex United Kingdom: Wiley-Blackwell.
Varelias, Antiopi, Bunting, Mark, Ormerod, Kate, Koyama, Motoko, Olver, Stuart, Straube, Jasmin, Kuns, Rachel, Robb, Renee, Henden, Andrea, Cooper, Leanne, Lachner, Nancy, Gartlan, Kate, Lantz, Olivier J., Kjer-Nielsen, Lars, Mak, Jeffrey, Fairlie, David, Clouston, Andrew, McCluskey, James, Rossjohn, Jamie, Lane, Steven, Hugenholtz, Phil and Hill, Geoff (2018). Recipient mucosal-associated invariant T cells control graft-versus-host-disease within the colon. Immunology Meeting, Austin Tx, 4-8 May 2018. Bethesda, MD United States: American Association of Immunologists.
Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P.A., Hugenholtz, Philip and Hill, Geoff R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Immunology 2017™ Meeting, Washington, DC United States, 12-16 May 2017. Rockville, MD United States: American Association of Immunologists. doi: 10.4049/jimmunol.198.supp.82.8
Moentadj, Rabia, Rehaume, Linda, Cuiv, Paraic O., Ormerod, Kate, Maradana, Muralidhara, Lakis, Vanessa Anne, Morrison, Mark, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2017). Streptococcus Species Enriched in the Oral Cavity of RA Patients: A Persistent Source of Peptidoglycan-Polysaccharide Polymers Which Drive Disseminated Synovial Inflammation. 2017 ACR/ARHP Annual Meeting, San Diego CA, United States, 3–8 November 2017. Hoboken, NJ United States: John Wiley & Sons. doi: 10.1002/art.40321
Budden, Kurtis, Gellatly, Shaan, Wood, David, Morrison, Mark, Cooper, Matthew, Dennis, Paul G., Hugenholtz, Philip and Hansbro, Philip (2017). Dietary fibre and microbial metabolites protect against cigarette smoke-induced lung pathology in mice. 22nd Congress of the Asian Pacific Society of Respirology, Sydney, Australia, 23–26 November 2017. Hoboken, NJ United States: Wiley.
Rehaume, Linda, Matigian, Nicholas, Ormerod, Kate, Kang, Alicia, Linedale, Richard, Zbarskaya, Olga, Kikly, Kristine, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip, Morrison, Mark, Le Cao, Kim-Anh and Thomas, Ranjeny (2017). IL-23 promotes fecal microbiota dysbiosis associated with susceptibility to spondyloarthritis and ileitis in ZAP-70 mutant SKG mice. ACR/ARHP Annual Meeting, San Diego, CA United States, 3-8 November 2017. Hoboken, NJ United States: John Wiley & Sons.
Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A., Hugenholtz, Philip and Hill, Geoff R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Immunology Meeting, Washington DC, 12-16 May 2017. Bethesda, MD United States: American Association of Immunologists.
Benham, Helen, Wood, John, Nagl, Lisa, Maradana, Muralidhara, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip and Thomas, Ranjeny (2016). An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factors. Australian Rheumatology Association in conjunction with Rheumatology Health Professionals Association, 57th Annual Scientific Meeting, Darwin, NT, Australia, 30 April–4 May 2016. Richmond, VIC, Australia: Wiley-Blackwell Publishing Asia. doi: 10.1111/imj.13052
Robinson, N., Brackin, R., Paungfoo-Lonhienne, C., Lonhienne, T., Westermann, M., Salazar, M., Yeoh, Y. K ., Hugenholtz, P., Ragan, M. A., Redding, M., Pratt, C., Wang, W. J., Royle, A., DiBella, L., Lakshmanan, P. and Schmidt, S. (2016). Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef. International Nitrogen Initiative Conference, Melbourne, Australia, 4-8 December 2016. Melbourne, Australia: International Nitrogen Initiative.
Gellatly, S., Dennis, P., Jarnicki, A., Lachner, N., Wood, D., Fricker, M., Budden, K., Liu, G., Keely, S., Morrison, M., Willner, D., Cooper, M., Hugenholtz, P. and Hansbro, P. (2016). Healthy gut microbiota ameliorates experimental chronic obstructive pulmonary disease. Annual Scientific Meeting of the Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science 2014, Perth, WA, Australia, 1–6 April 2016. Hoboken, NJ United States: Wiley. doi: 10.1111/resp.12754_22
Rehaume, L. M., Kang, A., Zbarskaya, O., Mullaney, J. A., Kim, M., Cuiv, O. P., Angel, N., Lachner, N., Daly, J., Morrison, M., Hugenholtz, P. and Thomas, R. (2016). Profiling immunogenic bacteria within the microbiota of SKG mice associated with spondyloarthritis and ileitis using IgA-SEQ. International Congress of Immunology (ICI 2016), Melbourne, Australia, 21-26 August 2016. Weinheim, Germany: Wiley.
Rehaume, Linda, Matigian, Nicholas, Kang, Alicia, Zbarskaya, Olga, Kikly, Kristine, Lachner, Nancy, Daly, Joshua, Hugenholtz, Philip, Morrison, Mark, Le Cao, Kim-Anh and Thomas, Ranjeny (2016). Treatment of ZAP-70 Mutant SKG Mice with Anti-IL-23 Antibody Alters Fecal Microbiota Composition and Prevents Outgrowth of Bacteria Associated with Susceptibility to Spondyloarthritis and Ileitis. 2016 ACR/ARHP Annual Meeting, Washington, DC United States, 11–16 November 2016 . Hoboken, NJ United States: Wiley.
Benham, Helen, Maradana, Muralidhara, Lakis, Vanessa Anne, Cuiv, Paraic O., Wood, John, Nagl, Lisa, Rammouth, Nishta, Owens, Clare, Daly, Joshua., Lachner, Nancy, Morrison, Mark, Hugenholtz, Philip, Le Cao, Kim-Anh and Thomas, Rarljeny (2016). Distinct Oral and Fecal Community Profiles Enriched in Opportunistic Pathogens in RA Patients and First Degree Relatives Are Influenced By Environmental Risk Factors, Including Smoking, Dental History and Lung Infection. 2016 ACR/ARHP Annual Meeting, Washington, DC, 11-16 November 2016. Hoboken, NJ, United States: John Wiley & Sons.
Pelzer, Elise, Hugens, Flavia, Hugenholtz, Philip, Lourie, Rohan, Beagley, Kenneth and Turner, Ross (2015). The placental microbiome; microbial presence in nature’s transplant. unknown, unknown, unknown. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2015.07.252
Ragonesi, Leanne, Huygens, Flavia, Turner, Ross, Hugenholtz, Philip, Lourie, Rohan, Beagley, Ken and Pelzer, Elise (2015). The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiome. unknown, unknown, unknown. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2015.07.308
Rehaume, Linda, Kang, Alicia, Zbarskaya, Olga, Mullaney, Jane, Kim, Matthew, Cuiv, Paraic O., Angel, Nicola, Hugenholtz, Philip, Morrison, Mark and Thomas, Ranjeny (2015). Profiling Immunogenic Bacteria within the Microbiota of ZAP-70 Mutant SKG Mice Associated with Spondyloarthritis and Ileitis Using IgA-SEQ. 2015 ACR/ARHP Annual Meeting, San Francisco, CA, United States, 6-11 November 2015. Hoboken, NJ, United States: John Wiley & Sons.
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy, Tyson, Gene W., Hugenholtz, Philip and Schembri, Mark A. (2014). Embedding Undergraduate Research throughout Microbiology Majors. ASM Conference for Undergraduate Educators, Danvers, MA United States, 15-18 May 2014.
Fangrath, S, Mudge, S., Deng, Y, Robinson, N, Schmidt, S, Hugenholtz, P, Ragan, M and Paungfoo-Lonhienne, C (2014). Plant growth promoting rhizobacteria (PGPR) for use in horticulture.. The 29th International Horticultural Congress, Brisbane Convention Centre, Brisbane Qld, Australia, 17 - 22 August 2014.
Willner, D., Ab-Ghani, N. A., Yerkovich, S., Tan, M. E., Hopkins, P. M., Chambers, D. C. and Hugenholtz, P. (2013). Longitudinal holistic profiling of the lung transplant microbiome. 33rd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation, Montreal, Canada, 24-27 April 2013. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.healun.2013.01.004
Lu, Y., Slater, F., Bello Mendoza, R., Jensen, P., Hugenholtz, P. and Batstone, D. J. (2013). Granule shearing enables the high resolution microbial identity. 13th World Congress on Anaerobic Digestion (AD 13), Santiago de Compostela, Spain, 25-28 June, 2013. London, United Kingdom: International Water Association (IWA).
Willner, D., Hugenholtz, P., Tan, M.E., Yerkovich, S.T., Hopkins, P.M. and Chambers, D.C. (2012). Distinct microbial signatures of healthy and failing lung allografts. 32nd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation/Meeting of the ISHLT Academy Core Competencies in Mechanical Circulatory Support, Prague, Czech Republic, 17-21 April 2012. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.healun.2012.01.072
Hugenholtz, Philip (2010). Is the future of metagenomics, genomics?. Experimental Biology 2010, Anaheim, CA, United States, 24-28 April 2010. Hoboken, NJ, United States: John Wiley & Sons.
Kristiansson, E., Hugenholtz, P. and Dalevi, D. (2010). ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg Sweden, Jun 26-Jul 01, 2010. MALDEN: WILEY-BLACKWELL PUBLISHING, INC.
Knierim, Bernhard, Wilmes, Paul, Webb, Rick I., McDonald, Kent, Comolli, Luis, Luef, Birgit, Downing, Kenneth H., Banfield, Jill, Hugenholtz, Phil, Liphardt, Jan and Auer, Manfred (2010). Correlative TEM/FISH imaging of microbial communities. *, *, *. St. Louis, MO, United States: Cell Press. doi: 10.1016/j.bpj.2009.12.3157
Pope, P., Denman, S., Tringe, S., Hinds, L., Hugenholtz, P., McSweeney, C. and Morrison, M. (2009). Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).. 2009 Conference on Gastrointestinal Function, Chicago, USA, 20-22 April, 2009. New York, NY, United States: Springer. doi: 10.1007/s00248-009-9496-x
Yannarell, A. C., Hess, M., Hugenholtz, P. and Mackie, R. I. (2009). Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen. Conference on Gastrointestinal Function, Chicago, USA, 20–22 April 2009. New York, NY United States: Springer. doi: 10.1007/s00248-009-9496-x
Dalevi, Daneil, Ivanova, Natalia N., Mavromatis, Konstantinos, Hooper, Sean D., Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos C. and Markowitz, Victor M. (2008). Annotation of metagenome short reads using proxygenes. Joint Meeting of the 7th European Conference on Computational Biology and the 5th Meeting of the Bioinformatics Italian Society (ECCB 2008), Cagliari, Italy, 22-26 September 2008. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btn276
Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system. 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, 6-10 August 2006. Oxford, U.K.: Oxford University Press. doi: 10.1093/bioinformatics/btl217
Martín, Héctor García, Kunin, Victor, Ivanova, Natalia, Warnecke, Falk, Peterson, S. B., Barry, Kerrie, McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf, Szeto, Ernest, Dalin, Eileen, Putnam, Nik, Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of phosphorus removing sludge communities. ISME Vienna 2006: 11th International Symposium on Microbial Ecology. The hidden powers: Microbial communities in action, Vienna, Austria, 20-25 August 2006. Kenes International.
Park, JW, Hill, P, Hugenholtz, P, Chung, N and Jung, F (2004). Magnetocardiography predicts coronary artery disease in patients presenting with acute chest pain. In: ESC Congress 2004, Munich Germany, (303-304). Aug 28-Sep 01, 2004.
Baldauf, SL, Bhattacharya, D, Cockrill, J, Hugenholtz, P, Pawlowski, J and Simpson, AGB (2004). The tree of life - An overview. Conference on Assembling the Tree of Life, New York Ny, May 30-Jun 01, 2002. NEW YORK: OXFORD UNIV PRESS.
Blackall, L. L., Hall, S. J., Hugenholtz, P., Keller, J. and Siyambalapitiya, N. (2000). Real-Time PCR: Can it accurately assess specific members in a mixed microbial community. 4th Annual Australian Environmental Engineering Research Event, Victor Harbor, South Australia, Australia, 21-24 November, 2000. Australia: EERE Organising Committee.
Hugenholtz, Phil (2000). Diverted Cultivation of Phylogenetically Novell Bacteria. ICCC9 9th International Congress for Culture Collections, Brisbane, Australia, 23-28 July, 2000. Australia: UQ Press/World Federation for Culture Studies.
Blackall, L. L., Bond, P. L., Burrell, P. C., Crocetti, G. and Hugenholtz, P. (1999). The microbiology of biological nutrient removal - latest discoveries and developments. IBC Conference on Advanced Wastewater and Sludge Treatment, Sydney, Australia, 27-28 Jan 1999. not available: not available.
Blackall, L. L., Bond, P. L., Crocetti, G., Hugenholtz, P., Jenkins, D., Keller, J. and Schuler, A. (1999). The determination of the bacteria involved in biological phosphorus removal from wastewater. IXth International Congress of Bacteriology and Applied Microbiology, Sydney, August 2-6, 1999.
Soddell, JA, Seviour, RJ, Blackall, LL and Hugenholtz, P (1998). New foam-forming nocardioforms found in activated sludge. 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley California, Jul 21-23, 1997. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. doi: 10.1016/S0273-1223(98)00151-6
Blackall, L. L., Burrell, P. C., Gwilliam, H., Bradford, D., Bond, P. L. and Hugenholtz, P. (1998). The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities. In: 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley, CA, United States, (451-454). 21-23 July 1997. doi:10.2166/wst.1998.0691
Blackall, LL, Seviour, EM, Bradford, D, Stratton, HM, Cunningham, MA, Hugenholtz, P and Seviour, RJ (1996). Towards understanding the taxonomy of some of the filamentous bacteria causing bulking and foaming in activated sludge plants. 18th Biennial Conference of the International-Association-on-Water-Quality, Singapore Singapore, Jun 23-28, 1996. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. doi: 10.1016/0273-1223(96)00639-7
Data Collection
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material. Cold Spring Harbor Laboratory Press. (Dataset) doi: 10.14264/uql.2016.841
Research Report
Oehmen, Christopher S., Sofia, Heidi J., Baxter, Douglas, Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos, Markowitz, Victor and Straatsma, Tjerk P. (2007). Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond. Oak Ridge, TN, United States: Office of Scientific and Technical Information (OSTI). doi: 10.2172/960403
Thesis
Hugenholtz, Philip (1994). An ecological and phylogenetic investigation of a bacterial biofilm growing on the cooling coils in an air-handling system. PhD Thesis, School of Molecular and Microbial Sciences, The University of Queensland. doi: 10.14264/uql.2015.257